SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data

BACKGROUND: Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. METHODS: In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. RESULTS: The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. CONCLUSIONS: SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. AVAILABILITY AND IMPLEMENTATION: SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/

Optimizing diffusion in multiplexes by maximizing layer dissimilarity

Diffusion in a multiplex depends on the specific link distribution between the nodes in each layer, but also on the set of the intralayer and interlayer diffusion coefficients. In this work we investigate, in a quantitative way, the efficiency of multiplex diffusion as a function of the topological similarity among multiplex layers. This similarity is measured by the distance between layers, taken among the pairs of layers. Results are presented for a simple two-layer multiplex, where one of the layers is held fixed, while the other one can be rewired in a controlled way in order to increase or decrease the interlayer distance. The results indicate that, for fixed values of all intra- and interlayer diffusion coefficients, a large interlayer distance generally enhances the global multiplex diffusion, providing a topological mechanism to control the global diffusive process. For some sets of networks, we develop an algorithm to identify the most sensitive nodes in the rewirable layer, so that changes in a small set of connections produce a drastic enhancement of the global diffusion of the whole multiplex system

Biological control of Aedes albopictus (Diptera: Culicidae) larvae in trap tyres by Mesocyclops longisetus (Copepoda: Cyclopidae) in two field trials

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POSIÇÃO DA ENFERMAGEM NO CONTINUUM OCUPAÇÃO-PROFISSIONALIZAÇÃO E A EXPANSÃO DA ESPECIALIZAÇÃO

Reflecting on the Nursing practice, we consider important to analyze the professionalization process pointing out the occupation and profession concept. All this lead us to the right of somebody to receive a professional designation and the nursing social status in the continuum occupation-professionalization, from the point of view of the called "sociologists of the professions". The objectives of the article are to concept occupation, profession, professional, and professionalization and to reflect on the Nursing professionalization process according to the point of view of the "sociologists of the professions" focusing on the specialization at the same time. We conclude that the Nursing has a body of specific knowledge in construction and some questions of the professionalization process need to be reviewed. That is for instance, the specialization question, since it does not exist any official policy that regulates the respect for the nurse specialty when it concerns the practical field. As many times is placed in very different sectors of its specialty.Reflexionando sobre la práctica de Enfermería, consideramos importante analizar el proceso de profesionalización situando el concepto de profesión y de ocupación, resultando de ahí el derecho de alguien recibir la designación de profesional; y la posición social de la enfermería en el continuum ocupación-profesionalización, desde el punto de vista de los llamados “sociólogos de las profesiones”. Los objetivos del artículo fueron: conceptuar ocupación, profesión, profesional y profesionalización y reflexionar sobre el proceso de profesionalización de Enfermería desde el punto de vista de los “sociólogos de las profesiones” enfocando paralelamente la especialización. Concluimos que la Enfermería posee un cuerpo de conocimiento específico en construcción y que algunas cuestiones del proceso de profesionalización deben ser revisadas, como es la cuestión de la especialización, ya que no existe ninguna política oficial que regule el respeto a la especialidad de la enfermera, siendo en la práctica, muchas veces, destinada a sectores totalmente diferentes de los de su especialidad.Refletindo sobre a prática de Enfermagem, consideramos importante analisar o processo de profissionalização situando o conceito de profissão e de ocupação, resultando daí o direito de alguém receber a designação de profissional; e a posição social da enfermagem no continuum ocupação-profissionalização, sob o ponto de vista dos chamados “sociólogos das profissões”. Os objetivos do artigo foram: conceituar ocupação, profissão, profissional e profissionalização e refletir sobre o processo de profissionalização da Enfermagem sob o ponto de vista dos “sociólogos das profissões” focalizando paralelamente a especialização. Concluímos que a Enfermagem possui um corpo de conhecimento específico em construção e que alguns quesitos do processo de profissionalização devem ser revistos, como é a questão da especialização, visto que não existe nenhuma política oficial que regule o respeito à especialidade da enfermeira quando ela vai para o campo prático, sendo muitas vezes alocadas em setores totalmente diferentes do de sua especialidade

Profile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus

<p>Abstract</p> <p>Background</p> <p>In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some groups of viruses. However, nothing is known about the vsRNAs produced during infections of members of the economically important family <it>Luteoviridae</it>, a group of phloem-restricted viruses. Here, we report the characterization of a population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus <it>Polerovirus</it>, family <it>Luteoviridae</it>.</p> <p>Results</p> <p>Deep sequencing of small RNAs (sRNAs) from leaves of CLRDV-infected cotton plants revealed that the vsRNAs were 21- to 24-nucleotides (nt) long and that their sequences matched the viral genome, with higher frequencies of matches in the 3- region. There were equivalent amounts of sense and antisense vsRNAs, and the 22-nt class of small RNAs was predominant. During infection, cotton <it>Dcl </it>transcripts appeared to be up-regulated, while Dcl2 appeared to be down-regulated.</p> <p>Conclusions</p> <p>This is the first report on the profile of sRNAs in a plant infected with a virus from the family <it>Luteoviridae</it>. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAs. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpectedly high accumulation of 22-nt vsRNAs are discussed. CLRDV is the causal agent of Cotton blue disease, which occurs worldwide. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases.</p

Benznidazole biotransformation and multiple targets in <i>Trypanosoma</i> cruzi revealed by metabolomics

&lt;b&gt;Background&lt;/b&gt;&lt;p&gt;&lt;/p&gt; The first line treatment for Chagas disease, a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, involves administration of benznidazole (Bzn). Bzn is a 2-nitroimidazole pro-drug which requires nitroreduction to become active, although its mode of action is not fully understood. In the present work we used a non-targeted MS-based metabolomics approach to study the metabolic response of T. cruzi to Bzn.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methodology/Principal findings&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Parasites treated with Bzn were minimally altered compared to untreated trypanosomes, although the redox active thiols trypanothione, homotrypanothione and cysteine were significantly diminished in abundance post-treatment. In addition, multiple Bzn-derived metabolites were detected after treatment. These metabolites included reduction products, fragments and covalent adducts of reduced Bzn linked to each of the major low molecular weight thiols: trypanothione, glutathione, γ-glutamylcysteine, glutathionylspermidine, cysteine and ovothiol A. Bzn products known to be generated in vitro by the unusual trypanosomal nitroreductase, TcNTRI, were found within the parasites, but low molecular weight adducts of glyoxal, a proposed toxic end-product of NTRI Bzn metabolism, were not detected.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions/significance&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Our data is indicative of a major role of the thiol binding capacity of Bzn reduction products in the mechanism of Bzn toxicity against T. cruzi