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.

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.

Integration in new product development: Case study in a large Brazilian high-technology company

Proficiency in management activities undertaken in product development processes is regarded as a key competitive advantage for companies, particularly for high-tech industrial firms, which benefit from the important competitiveness factor of launching products with a differentiated technological content. This paper's objective was to identify, through case study, practices for integration between the roles of R & D with others involved in product development in a large Brazilian company of industrial automation. The results suggest some management practices to improve the integration in new products development, such as the use of employees from marketing with knowledge and experience previously gained from R & D activities and uses the heavyweight product manager to solve synchronization problems between product and technology development. © Universidad Alberto Hurtado, Facultad de Economía y Negocios.

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.

Formation of silver chloride nanocrystals as a corrosion product of silver in H2SO4 solution

The purpose of this study is to characterize the corrosion product on the surface of silver, employing H2SO4 (0.5M) as electrolyte. The electrochemical parameters, Ecor, Icor, V cor and Rp were obtained after analyzing the potentiodynamic polarization curve in which two peaks were observed. The smallest (passive region) is attributed to the Cl- traces from the reference electrode, with micro-cracks. The second peak (in the transpassivation region) corresponds to the polarization curve of silver in H2SO 4 without contaminants. SEM images and EDS analysis reveal images of a surface layer on silver, consisting of structures containing sulfur, oxygen, silver and chloride, as the corrosion product. On this layer silver sulfate crystals were observed, which occurs during the formation of silver chloride nanocrystals with different morphologies, when chloride ions were added to the electrolyte medium. ©The Electrochemical Society.

Regions as the product of social construction

Includes bibliography

Peru: integration, sectoral specialization and synchronization with international gross domestic product cycles

Includes bibliography

Enzyme effects on extruded diets for dogs with soybean meal as a substitute for poultry by-product meal

The effects of exogenous enzymes supplementation on kibble diets for dogs formulated with soybean meal (SBM) as a substitute for poultry by-product meal (PM) was investigated on nutrient digestibility, fermentation products formation, post-prandial urea response and selected faecal bacteria counts. Two kibble diets with similar compositions were used in two trials: PM-based diet (28.9% of PM; soybean hulls as a fibre source) and SBM-based diet (29.9% of SBM). In experiment 1, the SBM diet was divided into three diets: SBM-0, without enzyme addition; SBM-1, covered after extrusion with 7500U protease/kg and 45U cellulase/kg; and SBM-2, covered with 15000U protease/kg and 90U cellulase/kg. In experiment 2, the SBM diet was divided into three diets: SBM-0; SBM-1, covered with 140U protease/kg; 8U cellulase/kg, 800U pectinase/kg, 60U phytase/kg, 40U betaglucanase/kg and 20U xylanase/kg; and SMB-2, covered with 700U protease/kg, 40U cellulase/kg, 4000U pectinase/kg, 300U phytase/kg, 200U betaglucanase/kg and 100U xylanase/kg. Each experiment followed a block design with six dogs per diet. Data were submitted to analysis of variance and means compared by orthogonal and polynomial contrasts (p<0.05). In both experiments, nutrients and energy digestibility did not differ between diets (p>0.05). SBM consumption resulted in increased faecal moisture and production (p<0.05), without effect on faecal score. Higher concentration of propionate, acetate and lactate, and lower ammonia and pH were found in the faeces of dogs fed SBM (p<0.05). Higher post-prandial urea was verified in dogs fed SBM (p<0.05). In experiment 2, the addition of enzymes increased faecal concentration of propionate, acetate and total short-chain fatty acid (p<0.05) and tended to reduce post-prandial urea concentration (p=0.06). Although with similar digestibility, SBM shows a worse utilization of absorbed amino acids than the PM. Soybean oligosaccharides can beneficially change gut fermentation product formation. Enzymes can increase the gut fermentation activity and improve the SBM proteic value. © 2013 Blackwell Verlag GmbH.

Screening of genomic libraries

Microsatellites, or simple sequence repeats (SSRs), have proven to be an important molecular marker in plant genetics and breeding research. The main strategies to obtain these markers can be through genomic DNA and from expressed sequence tags (ESTs) from mRNA/cDNA libraries. Genetic studies using microsatellite markers have increased rapidly because they can be highly polymorphic, codominant markers and they show heterozygous conserved sequences. Here, we describe a methodology to obtain microsatellite using the enrichment library of DNA genomic sequences. This method is highly efficient to development microsatellite markers especially in plants that do not have available ESTs or genome databases. This methodology has been used to enrich SSR marker libraries in Citrus spp., an important tool to genotype germplasm, to select zygotic hybrids, and to saturate genetic maps in breeding programs. © Springer Science+Business Media, LLC 2013.

When less is better: Insights from the product mix dilemma from the Theory of Constraints perspective

Perhaps due to its origins in a production scheduling software called Optimised Production Technology (OPT), plus the idea of focusing on system constraints, many believe that the Theory of Constraints (TOC) has a vocation for optimal solutions. Those who assess TOC according to this perspective indicate that it guarantees an optimal solution only in certain circumstances. In opposition to this view and founded on a numeric example of a production mix problem, this paper shows, by means of TOC assumptions, why the TOC should not be compared to methods intended to seek optimal or the best solutions, but rather sufficiently good solutions, possible in non-deterministic environments. Moreover, we extend the range of relevant literature on product mix decision by introducing a heuristic based on the uniquely identified work that aims at achieving feasible solutions according to the TOC point of view. The heuristic proposed is tested on 100 production mix problems and the results are compared with the responses obtained with the use of Integer Linear Programming. The results show that the heuristic gives good results on average, but performance falls sharply in some situations. © 2013 Copyright Taylor and Francis Group, LLC.

Product mix: The approach of throughput per day

Defining product mix is very important for organisations because it determines how productive resources are allocated among various operations. However, it is often defined subjectively. The methods commonly used for this definition are Integer Linear Programming and heuristics based in Theory of Constraints, which use maximum throughput as a performance measure. Although this measure provides maximum throughput to specific problem, it does not consider aspects of time, as days, utilised to make the throughput. Taking this into account, the aim of this paper is to present a throughput per day approach to define product mix, as well as to propose a constructive heuristic to help in this process. The results show that the proposed heuristic obtained satisfactory approximation when compared to the optimum values obtained by enumeration. © 2013 Copyright Taylor and Francis Group, LLC.

The use of NaOCl in combination with CHX produces cytotoxic product

Objectives: The combination of sodium hypochlorite (NaOCl) and chlorhexidine (CHX) yields a precipitate potentially toxic (PPT). The aim of this study was to evaluate the tissue response to implanted polyethylene tubes filled with PPT-soaked fibrin sponge. Methods: Forty rats received four polyethylene tubes each; each tube was filled with fibrin sponge soaked by 2.5 % NaOCl, 2.0 % CHX, PPT (2.5 % NaOCl plus 2.0 % CHX), or not soaked (control). The observation time points were 7, 15, 30, 60, and 90 days. At each time point, eight animals were killed, and the tubes and surrounding tissues were removed, fixed, and prepared for light microscopic analysis by performing glycol methacrylate embedding, serial cutting into 3-μm sections, and hematoxylin-eosin staining. Qualitative and quantitative evaluations of the reactions were performed. Results were statistically analyzed by Kruskal-Wallis test (p < 0.05). Results: All chemical solutions caused moderate reactions at 7 days. On day 30, PPT group was more cytotoxic than the control group and the CHX group (p < 0.05). On days 15 and 60, PPT group was more cytotoxic than the control group (p < 0.05). On day 90, there was no statistically significant difference between the different groups. Conclusion: PPT is more cytotoxic than NaOCl and CHX alone, particularly in the short term. Clinical significance: Protocols which suggest the use of CHX and NaOCl must be revised because this mixture produces cytotoxic product. © 2013 Springer-Verlag Berlin Heidelberg.

The historical relationship between energy-consumption and gross national product in the United States

Includes bibliography

Can overharvesting of a non-timber-forest-product change the regeneration dynamics of a tropical rainforest? The case study of Euterpe edulis

The exploitation of non-timber forest products is often considered a low-impact activity in tropical forests. However, assessments of the impacts of such activity are mostly focused on the harvested species and not on the plant community, thus limiting our understanding for establishing forest management recommendations. We investigated the consequences of Euterpe edulis palm heart harvesting on the seed rain in the Brazilian Atlantic rainforest. We compared the density of E. edulis individuals, as well as the density of E. edulis seeds, and the density, richness and functional composition of seed rain of the whole plant community, before and after palm heart harvesting in a 10 ha permanent plot. This assessment was carried out in preserved (typical old-growth Atlantic rainforest) and in disturbed (more open habitat dominated by the native bamboo Guadua tagoara) forest patches. Palm harvesting reduced the E. edulis population from 202.16 to 25.67 ind/ha and its seed rain density from 0.362 to 0.3 seeds/m2 and from 2.395 to 0.15 seeds/m2 in preserved and disturbed forest patches, respectively. Seed density of light-dependent climbers, pioneer trees, bamboo and animal-dispersed seeds increased after palm harvesting, especially in the disturbed forest patches, where palm harvesting was more intense and may have changed the light regime of the understory. On the other hand, species richness of the plant community declined by half. We observed a remarkable decline in the number of animal-dispersed species, especially for those with large seeds, suggesting that the activity of seed dispersers, including many species attracted by E. edulis fruits, was reduced. Therefore, harvesting of E. edulis palm heart may change the regeneration dynamics of the Atlantic rainforest, both due to shifts in forest structure, mediated by the removal of individuals from the forest canopy, and in community functioning, mediated by the interference on the activity of seed dispersers. © 2013 Elsevier B.V. All rights reserved.