Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98 % minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65(.)2 %) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10(.)9 %), Spirochaetes (4(.)3 %), Bacteroidetes (6(.)5 %), Actinobacteria (2(.)2 %) and Deferribacteres (2(.)2 %). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

Camponeses Brazil's Peasant Movement in Historical Perspective (1946-2004)

Comparison of the histories of three leading peasant organizations in the Pontal do Paranapanema region of Brazil-the Partido Comunista do Brasil (PCB) from 1945 to 1964, the Confederacao Nacional de Trabalhadores na Agricultura (CONTAG) from 1964 to 1984, and the Movimento dos Trabalhadores Rurais Sem-Terra (MST) from 1984 to 2004-suggests that continuity is as important as change in understanding Brazilian peasant movements. The MST has been considered a "new social movement" in that it has eschewed partisan politics, incorporated families as members rather than just male heads of household, had a national scope and a participatory decision-making structure, and been attuned to the international struggle over globalization. Placing it in historical perspective makes it clear, however, that this is not the first time that militants have organized around the concept of peasants as a political identity; that while the representation of peasants in the leadership of contemporary rural labor organizations may be greater than in the past, earlier peasant leaders also struggled on behalf of their class; that earlier peasant organizations had, if not a national presence, a substantial presence in the agricultural states of the time; and that attempts at international organization to unite peasant struggles around the globe are not entirely new. This is not to deny the innovative features of contemporary movements but to suggest that the investigation of past achievements will contribute to a fuller appreciation of these movements' conditions and prospects.

Ceramic materials in dentistry: historical evolution and current practice

Dental ceramics are presented within a simplifying framework allowing for facile understanding of their development, composition and indications. Engineering assessments of clinical function are dealt with and literature is reviewed on the clinical behaviour of all-ceramic systems. Practical aspects are presented regarding the choice and use of dental ceramics to maximize aesthetics and durability, emphasizing what we know and how we know it.

Optimal clone identifier for genomic shotgun libraries: OC Identifier tool

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray. ©FUNPEC-RP.

Open urban spaces quality: A study in a historical square in Bath - UK

The quality of open urban spaces is very important for urban vitality. Nowadays urban designers have to face the great challenge of designing urban spaces able to respond to people's need for liveable spaces. The success of these spaces depends on various aspects and the microclimatic condition has been recognized as one of the most influential. However, studies on thermal comfort in open space have shown that the user's thermal sensation does not depend only on microclimate parameters but also on other local qualitative aspects. Thus, environmental quality evaluation of successful public spaces can contribute to understand this issue. This paper focuses on a case study regarding Queen Square's environmental quality, a public space of historical importance in Bath-UK. The first stage of the research, a study on local characteristics and people observations, allowed a preliminary evaluation of the space performance, their social aspects, while it characterized and quantified the hourly variation of the space use in different days and seasons. In the second stage, short microclimatic surveys were carried out simultaneously with a perception survey through a questionnaire. The results show the strong vitality of the square and socioenvironmental significance, not only for its location in the urban context, but also for its historical value. The environmental quality of the square contributes to the users' sensation of comfort even in adverse climatic conditions. This research is part of a project that aims to investigate the impact of the environmental stimuli in the use of open spaces and intend to develop design strategies that aim to maximise the use of open spaces in different weather conditions.

Routine libraries for pattern recognition in quasispecies.

The results obtained through biological research usually need to be analyzed using computational tools, since manual analysis becomes unfeasible due to the complexity and size of these results. For instance, the study of quasispecies frequently demands the analysis of several, very lengthy sequences of nucleotides and amino acids. Therefore, bioinformatics tools for the study of quasispecies are constantly being developed due to different problems found by biologists. In the present study, we address the development of a software tool for the evaluation of population diversity in quasispecies. Special attention is paid to the localization of genome regions prone to changes, as well as of possible hot spots.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

Historical and recent biological markers of exposure to fluoride

Recent and historical biomarkers assess chronic or subchronic exposure to fluoride. The most studied recent biomarkers are nails and hair. Both can be non-invasively obtained, although collection of nails is more accepted by the subjects. External contamination may be a problem for both biomarkers and still needs to be better evaluated. Nails have been more extensively studied. Although the available knowledge does not allow their use as predictors of dental fluorosis by individual subjects, since reference values of fluoride have not yet been established, they have a strong potential for use in epidemiological surveys. Toenails should be preferred instead of fingernails, and variables that are known to affect nail fluoride concentrations - such as age, gender and geographical area - should be considered. The main historical biomarkers that could indicate total fluoride body burden are bone and dentin. Of these, bone is more studied, but its fluoride concentrations vary according to the type of bone and subjects' age and gender. They are also influenced by genetic background, renal function and remodeling rate, variables that complicate the establishment of a normal range of fluoride levels in bone that could indicate 'desirable' exposure to fluoride. The main issue when attempting to use bone as biomarker of fluoride exposure is the difficulty and invasiveness of sample collection. In this aspect, collection of dentin, especially from 3rd molars that are commonly extracted, is advantageous. However, mean values also span a wide range and reference concentrations have not been published yet. © 2011 S. Karger AG, Basel.

The University and its libraries: Reactions and resistance to scientific publishers

This paper addresses the relationship of copyright and the right of universities on scientific production. Information and Communication Technologies (ICTs) are causing many changes in the system of scientific communication, such as the creation of Institutional Repositories that aim to gather scientific production in digital format. The University needs quicker ways of spreading academic production and many questions are emerging due to contexts such as the Open Access movement. Thus, this paper questions the positioning of Universities, especially Public Universities, which despite having policies related to intellectual property to protect the transferring forms of research results to society; many times do not have a positioning or a mechanism that regulates the self-deposit of scientific production in these Institutional Repositories. In order to develop this paper, the following issues are addressed: lack of interest of the University in storing scientific production; reports on the relationship of the library with scientific publishing houses; the participation of faculty members and students in supporting the Free Access movement; and initiatives aimed at greater flexibility of copyright to the context of scientific production. In order to follow the development of these issues at international level, it was opted for qualitative research with non-participating direct observation to carry out the identification and description of copyright policy of important publishers from the ROMEO SHERPA site; therefore, it can be observed that there are changes regarding the publishers' flexibility before self-archiving of authors in open access institutional repositories in their universities. Given this scenario, we presente reflections and considerations that involve the progress and mainly the integration of the University and its faculty members; the institution should recommend and guide its faculty members not to transfer their copyrights, but to defend their right of copy to Institutional Repositories along with Publishing Houses.

Mexico's market reforms in historical perspective

Includes bibliography

ECLAC in its historical setting

Includes bibliography

The future of the international railways of South America: a historical approach

Includes bibliography

A historical turning point for the Latin American periphery

Includes bibliography