Multiple domain insertions and losses in the evolution of the Rab prenylation complex

<p>Abstract</p> <p>Background</p> <p>Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase – RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear.</p> <p>Results</p> <p>We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in detail the domain structure of all these components and the phylogenetic relationships between the individual domains.</p> <p>Conclusion</p> <p>We found different domain insertions in different taxa, in α-subunits of RGGTase and REP. Our results suggest that there were multiple insertions, expansions and contractions in the evolution of this prenylation complex.</p

Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde

This deposit is composed by the main article plus the supplementary materials of the publication.The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poilão reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01’s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country’s microbial ecology as a whole of water reservoirs on the rise.Portuguese Science and Technology Foundation grants: (PTDC/MAR-BIO/4132/2014, SFRH/BD/113752/2015, SFRH/BPD/91518/2012).info:eu-repo/semantics/publishedVersio

Analysis of histopathological aspects in acquired middle ear cholesteatoma

Middle ear cholesteatomas are characterized by the presence of stratified squamous epithelium in this cavity with highly invasive properties causing bone destruction and it may lead to complications. AIM: To study the histopathological features in acquired cholesteatomas of the middle ear, correlating this data with patient age. Study design:clinical and experimental cross-sectional study. MATERIAL AND METHODS: Samples were obtained from 50 patients submitted to otologic surgery for the removal of middle ear cholesteatomas from 2006 to 2007. Thirty four patients were adults and 16 were children. Samples were studied by histological analysis. RESULTS: we found the presence of epithelial atrophy (78%), epithelial acanthosis (88%), hyperplasia of the basal layer (88%) and formation of epithelial cones (62%). There was a positive and significant correlation between histopathological variables (such as epithelial acanthosis, hyperplasia of the basal layer and formation of epithelial cones). Histopathological variables presented no statistical significant difference in both age groups (p>0,05). CONCLUSION: Cholesteatomas have hyperproliferating characteristics with epithelial acanthosis, hyperplasia of the basal layer and the presence of epithelial cones in the matrix.O colesteatoma da orelha média é caracterizado pela presença de epitélio estratificado pavimentoso queratinizado neste local, com alto poder invasivo, causando destruição óssea e podendo levar a complicações. OBJETIVO: Estudar os padrões histopatológicos no colesteatoma adquirido da orelha média. Correlacionar esses dados com a idade do paciente. FORMA DE ESTUDO: Clínico e experimental do tipo transversal. MATERIAL E MÉTODO: Foram colhidas amostras de colesteatoma de 50 pacientes submetidos à cirurgia otológica, sendo 34 adultos e 16 crianças, no período de 2006 a 2007. Essas amostras foram submetidas à análise histológica. RESULTADOS: A presença de atrofia foi encontrada em 78% dos casos, acantose em 88%, hiperplasia da camada basal em 88% e cones epiteliais em 62%. As correlações entre acantose e hiperplasia da camada basal, acantose e formação de cones epiteliais, hiperplasia da camada basal foram positivas e significativas. Não houve diferença estatisticamente significativa em relação aos padrões histopatológicos entre os dois grupos etários (p>0,05). CONCLUSÃO: O colesteatoma tem características hiperproliferativas, com acantose, hiperplasia da camada basal e presença de cones epiteliais na sua matriz.SCSP FCM Depto. MorfologiaUNIFESP-EPMSCSP FCM Depto. de OtorrinolaringologiaFundação Antônio PrudenteUNIFESP, EPMSciEL

Evolution of protein complexes by duplication of homomeric interactions.

BACKGROUND: Cellular functions are accomplished by the concerted actions of functional modules. The mechanisms driving the emergence and evolution of these modules are still unclear. Here we investigate the evolutionary origins of protein complexes, modules in physical protein-protein interaction networks. RESULTS: We studied protein complexes in Saccharomyces cerevisiae, complexes of known three-dimensional structure in the Protein Data Bank and clusters of pairwise protein interactions in the networks of several organisms. We found that duplication of homomeric interactions, a large class of protein interactions, frequently results in the formation of complexes of paralogous proteins. This route is a common mechanism for the evolution of complexes and clusters of protein interactions. Our conclusions are further confirmed by theoretical modelling of network evolution. We propose reasons for why this is favourable in terms of structure and function of protein complexes. CONCLUSION: Our study provides the first insight into the evolution of functional modularity in protein-protein interaction networks, and the origins of a large class of protein complexes

3D complex: a structural classification of protein complexes.

Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes

Aplicação de Modelos Intencionais e Sistemas Multiagentes para Estabelecer Políticas de Monitoração de Transparência de Software

O artigo apresenta uma proposta de monitoração de características de transparência de software a partir de sistemas multiagentes. É um primeiro esforço para o entendimento de políticas e modelos intencionais aplicados a agentes autônomos monitores

O ENSINO DE FÍSICA E A INCLUSÃO DE ESTUDANTES COM DEFICIÊNCIA

The teaching of physics is not a much explored topic, but its importance has grown in the context of the publication of the National Common Curricular Base (BNCC), which stipulates many topics directly related to physics so that everyone can use the basic education stage. Therefore, it becomes evident the importance of investigating the subject and presenting the main contributions on the teaching of physics in students with disabilities and investigating the main challenges faced by the teachers responsible for teaching. In view of the above, this research aims to present the teaching of physics and inclusion, through a literature review of qualitative nature and descriptive character.La enseñanza de la física no es un tema muy explorado, pero su importancia ha crecido en el contexto de la publicación de la Base Curricular Nacional Común (BNCC), que estipula muchos temas directamente relacionados con la física para que todos puedan utilizar la etapa de educación básica. Por lo tanto, se hace evidente la importancia de investigar el tema y presentar las principales contribuciones sobre la enseñanza de la física en estudiantes con discapacidad e investigar los principales desafíos que enfrentan los profesores responsables de la enseñanza. En vista de lo anterior, esta investigación tiene como objetivo presentar la enseñanza de la física y la inclusión, a través de una revisión de la literatura de naturaleza cualitativa y carácter descriptivo.  O ensino de física não é um tema muito explorado, mas sua importância cresceu no contexto da publicação da Base Nacional Comum Curricular (BNCC), que estipula muitos tópicos diretamente relacionados à física para que todos possam usar o estágio de educação básica. Portanto, torna-se evidente a importância de investigar o assunto e apresentar as principais contribuições sobre o ensino da física em estudantes com deficiência e investigar os principais desafios enfrentados pelos professores responsáveis ​​pela docência. Diante do exposto, esta pesquisa visa apresentar o ensino de física e a inclusão, através de uma revisão de literatura de cunho qualitativo e caráter descritivo.  O ensino de física não é um tema muito explorado, mas sua importância cresceu no contexto da publicação da Base Nacional Comum Curricular (BNCC), que estipula muitos tópicos diretamente relacionados à física para que todos possam usar o estágio de educação básica. Portanto, torna-se evidente a importância de investigar o assunto e apresentar as principais contribuições sobre o ensino da física em estudantes com deficiência e investigar os principais desafios enfrentados pelos professores responsáveis ​​pela docência. Diante do exposto, esta pesquisa visa apresentar o ensino de física e a inclusão, através de uma revisão de literatura de cunho qualitativo e caráter descritivo.

Searching for network modules

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a novel type of objective function for graph clustering, in the form of a multilinear polynomial whose coefficients are determined by network topology. It may be thought of as a potential function, to be maximized, taking its values on fuzzy clusterings or families of fuzzy subsets of nodes over which every node distributes a unit membership. When suitably parametrized, this potential is shown to attain its maximum when every node concentrates its all unit membership on some module. The output thus is a partition, while the original discrete optimization problem is turned into a continuous version allowing to conceive alternative search strategies. The instance of the problem being a pseudo-Boolean function assigning real-valued cluster scores to node subsets, modularity maximization is employed to exemplify a so-called quadratic form, in that the scores of singletons and pairs also fully determine the scores of larger clusters, while the resulting multilinear polynomial potential function has degree 2. After considering further quadratic instances, different from modularity and obtained by interpreting network topology in alternative manners, a greedy local-search strategy for the continuous framework is analytically compared with an existing greedy agglomerative procedure for the discrete case. Overlapping is finally discussed in terms of multiple runs, i.e. several local searches with different initializations.Comment: 10 page

The protective effect of Canova homeopathic medicine in cyclophosphamide-treated non-human primates

Background: Canova activates macrophages and indirectly induces lymphocyte proliferation. Here we evaluated the effects of Canova in cyclophosphamide-treated non-human primates.Methods: Twelve Cebus apella were evaluated. Four animals were treated with Canova only. Eight animals were treated with two doses of cyclophosphamide (50 mg/kg) and four of these animals received Canova. Body weight, biochemistry and hematologic analyses were performed for 40 days. Micronucleus and comet assays were performed for the evaluation of DNA damage.Results: We observed that cyclophosphamide induced abnormal WBC count in all animals. However, the group treated with cyclophosphamide plus Canova presented a higher leukocyte count than that which received only cyclophosphamide. Cyclophosphamide induced micronucleus and DNA damage in all animals. the frequency of these alterations was significantly lower in the Canova group than in the group without this medicine.Conclusions: Our results demonstrated that Canova treatment minimizes cyclophosphamide myelotoxicity in C. apella. (C) 2012 Elsevier B.V. All rights reserved.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo, Disciplina Genet, Dept Morfol & Genet, BR-04023900 São Paulo, BrazilUniv São Paulo, Dept Anal Clin Toxicol & Bromatol, Fac Ciencias Farmaceut Ribeirao Preto, BR-14040903 Ribeirao Preto, SP, BrazilFed Univ Para, Lab Citogenet Humana, Inst Ciencias Biol, BR-66059 Belem, Para, BrazilUniversidade Federal de São Paulo, Disciplina Ginecol, Dept Tocoginecol, BR-04039032 São Paulo, BrazilFed Univ Para, Serv Cirurgia, Hosp Univ Joao de Barros Barreto, BR-66073000 Belem, Para, BrazilMinist Saude, Ctr Nacl Primatas, BR-77030000 Ananindeua, PA, BrazilUniv Fed Piaui, Lab Genet & Biol Mol, BR-64202020 Parnaiba, PI, BrazilUniversidade Federal de São Paulo, Disciplina Genet, Dept Morfol & Genet, BR-04023900 São Paulo, BrazilUniversidade Federal de São Paulo, Disciplina Ginecol, Dept Tocoginecol, BR-04039032 São Paulo, BrazilCNPq: 550885/2007-2Web of Scienc