PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

The role of European "ro-ro" port terminals in the automotive supply chain management

The aim of this paper is concerned with the design and development of a functional framework for maritime mode integration in European automotive supply chain management when considering outbound distribution. Furthermore, it provides a readjustment of traditional concepts and terminology with findings that the role of ro-ro port terminals should be considered as decoupling points, poles and postponement platforms. Case studies examine relevant Western European ro-ro port terminals for cars and respective links to assembly/factories of vehicles localized in the hinterland and concludes that ro-ro port terminals reduce logistical friction and impedance, as well as promote space/time compression.

Besnoitia besnoiti protein disulfide isomerase (BbPDI): molecular characterization, expression and in silico modelling

Besnoitia besnoiti is an apicomplexan parasite responsible for bovine besnoitiosis, a disease with a high prevalence in tropical and subtropical regions and re-emerging in Europe. Despite the great economical losses associated with besnoitiosis, this disease has been underestimated and poorly studied, and neither an effective therapy nor an efficacious vaccine is available. Protein disulfide isomerase (PDI) is an essential enzyme for the acquisition of the correct three-dimensional structure of proteins. Current evidence suggests that in Neosporacaninum and Toxoplasmagondii, which are closely related to B. besnoiti, PDI play an important role in host cell invasion, is a relevant target for the host immune response, and represents a promising drug target and/or vaccine candidate. In this work, we present the nucleotide sequence of the B. besnoiti PDI gene. BbPDI belongs to the thioredoxin-like superfamily (cluster 00388) and is included in the PDI_a family (cluster defined cd02961) and the PDI_a_PDI_a'_c subfamily (cd02995). A 3D theoretical model was built by comparative homology using Swiss-Model server, using as a template the crystallographic deduced model of Tapasin-ERp57 (PDB code 3F8U chain C). Analysis of the phylogenetic tree for PDI within the phylum apicomplexa reinforces the close relationship among B. besnoiti, N. caninum and T. gondii. When subjected to a PDI-assay based on the polymerisation of reduced insulin, recombinant BbPDI expressed in E. coli exhibited enzymatic activity, which was inhibited by bacitracin. Antiserum directed against recombinant BbPDI reacted with PDI in Western blots and by immunofluorescence with B. besnoiti tachyzoites and bradyzoites.

Hydrogen peroxide sensing, signaling and regulation of transcription factors

The regulatory mechanisms by which hydrogen peroxide (H2O2) modulates the activity of transcription factors in bacteria (OxyR and PerR), lower eukaryotes (Yap1, Maf1, Hsf1 and Msn2/4) and mammalian cells (AP-1, NRF2, CREB, HSF1, HIF-1, TP53, NF-κB, NOTCH, SP1 and SCREB-1) are reviewed. The complexity of regulatory networks increases throughout the phylogenetic tree, reaching a high level of complexity in mammalians. Multiple H2O2 sensors and pathways are triggered converging in the regulation of transcription factors at several levels: (1) synthesis of the transcription factor by upregulating transcription or increasing both mRNA stability and translation; (ii) stability of the transcription factor by decreasing its association with the ubiquitin E3 ligase complex or by inhibiting this complex; (iii) cytoplasm-nuclear traffic by exposing/masking nuclear localization signals, or by releasing the transcription factor from partners or from membrane anchors; and, (iv) DNA binding and nuclear transactivation by modulating transcription factor affinity towards DNA, co-activators or repressors, and by targeting specific regions of chromatin to activate individual genes. We also discuss how H2O2 biological specificity results from diverse thiol protein sensors, with different reactivity of their sulfhydryl groups towards H2O2, being activated by different concentrations and times of exposure to H2O2. The specific regulation of local H2O2 concentrations is also crucial and results from H2O2 localized production and removal controlled by signals. Finally, we formulate equations to extract from typical experiments quantitative data concerning H2O2 reactivity with sensor molecules. Rate constants of 140 M-1s−1 and ≥ 1.3 × 103 M-1s−1 were estimated, respectively, for the reaction of H2O2 with KEAP1 and with an unknown target that mediates NRF2 protein synthesis. In conclusion, the multitude of H2O2 targets and mechanisms provides an opportunity for highly specific effects on gene regulation that depend on the cell type and on signals received from the cellular microenvironment.

Teatro no currículo: avaliar o quê e para quê?

Nalgumas áreas curriculares disciplinares, como o Teatro, as aprendizagens e as competências não se adquirem nem desenvolvem, em geral, de acordo com a díade de estratégias que os professores parecem privilegiar, isto é: transmissão do conhecimento e, pouco depois, confirmação – na maioria das vezes através da modalidade de escrita – da aprendizagem desse conhecimento pelos alunos. Note-se, porém, que, mesmo naquelas áreas que os responsáveis políticos distinguem com um “exame nacional”, como o Português, nem todas as aprendizagens promovidas e realizadas são testáveis numa prova escrita e no imediato (como, a título de exemplo, as que se inscrevem nos domínios da comunicação oral e da leitura em voz alta, também amplamente abordadas em Teatro). Às áreas da educação artística, e do Teatro em particular, os professores associam essencialmente – ou exclusivamente – a criatividade, a imaginação e a expressividade. Sendo, embora, competências potencialmente desenvolvidas e avaliadas também nas áreas da educação artística, não são um exclusivo destas áreas. Cada área curricular disciplinar do âmbito da educação artística – e o Teatro não é exceção – assenta numa específica linguagem artística, que integra conteúdos, estratégias, atividades, recursos, técnicas, conceitos e terminologias próprios, que as crianças, com vista ao seu desenvolvimento completo e harmonioso, têm o direito de aprender e desenvolver. Daqui decorrem algumas questões: O que – e como – avaliar nas áreas da educação artística, em particular no Teatro? Que princípios poderão estar inerentes a um dispositivo de avaliação em Teatro, em contexto curricular? Terão as modalidades de avaliação não escrita estatuto de fiabilidade? O binómio teatro/currículo encerra um paradoxo a que pretendemos dar atenção: embora nem sempre abordado com regularidade e seguindo uma lógica dedesenvolvimento curricular, o Teatro constitui, apesar disso, uma das estratégias privilegiadas pelos professores de participação em projetos e iniciativas formais, na maior parte das vezes de cariz pontual (como momentos festivos ou de apresentação à comunidade), em que os alunos são sujeitos ao juízo avaliativo dos públicos. Partindo dos princípios de que (i) em contexto curricular cada atividade tem uma intencionalidade e que (ii) a “educação” artística não visa a identificação ou a valorização de “talentos”, pretendemos defender a seguinte ideia: Só depois de estabelecermos inequivocamente os objetivos da nossa ação educativa-pedagógica e, por conseguinte, uma estratégia de avaliação, é que podemos definir um percurso com sentido. Esta comunicação de natureza teórica, cuja base reflexiva decorre de mais de vinte anos de intervenção em contextos escolares, tanto do ensino básico como de formação de professores, tentará formular questões e problematizar algumas linhas de pensamento, mais do que encontrar respostas, no sentido de suscitar, principalmente da parte dos professores, a necessidade de uma mudança de atitude e de práticas face ao teatro na escola.