Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Coconut, Cocos nucifera L. is a major plantation crop, which ensures income for millions of people in the tropical region. Detailed molecular studies on zygotic embryo development would provide valuable clues for the identification of molecular markers to improve somatic embryogenesis. Since there is no ongoing genome project for this species, coconut expressed sequence tags (EST) would be an interesting technique to identify important coconut embryo specific genes as well as other functional genes in different biochemical pathways. The goal of this study was to analyse the ESTs by examining the transcriptome data of the different embryo tissue types together with one somatic tissue. Here, four cDNA libraries from immature embryo, mature embryo, microspore derived embryo and mature leaves were constructed. cDNA was sequenced by the Roche-454 GS-FLX system and assembled into 32621 putative unigenes and 155017 singletons. Of these unigenes, 18651 had significant sequence similarities to non-redundant protein database, from which 16153 were assigned to one or more gene ontology categories. Homologue genes, which are responsible for embryo development such as chitinase, beta-1,3-glucanase, ATP synthase CF0 subunit, thaumatin-like protein and metallothionein-like protein were identified among the embryo EST collection. Of the unigenes, 6694 were mapped into 139 KEGG pathways including carbohydrate metabolism, energy metabolism, lipid metabolism, amino acid metabolism and nucleotide metabolism. This collection of 454-derived EST data generated from different tissue types provides a significant resource for genome wide studies and gene discovery of coconut, a non-model species.

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.

Predicating from an early age: edusemiotics and the potential of children’s preconceptions

This paper aims to explain how semiotics and constructivism can collaborate in an educational epistemology by developing a joint approach to prescientific conceptions. Empirical data and findings of constructivist research are interpreted in the light of Peirce’s semiotics. Peirce’s semiotics is an anti-psychologistic logic (CP 2.252; CP 4.551; W 8:15; Pietarinen in Signs of logic, Springer, Dordrecht, 2006; Stjernfelt in Diagrammatology. An investigation on the borderlines of phenomenology, ontology and semiotics, Springer, Dordrecht, 2007) and relational logic. Constructivism was traditionally developed within psychology and sociology and, therefore, some incompatibilities can be expected between these two schools. While acknowledging the differences, we explain that constructivism and semiotics share the assumption of realism that knowledge can only be developed upon knowledge and, therefore, an epistemological collaboration is possible. The semiotic analysis performed confirms the constructivist results and provides a further insight into the teacher-student relation. Like the constructivist approach, Peirce’s doctrine of agapism infers that the personal dimension of teaching must not be ignored. Thus, we argue for the importance of genuine sympathy in teaching attitudes. More broadly, the article also contributes to the development of postmodern humanities. At the end of the modern age, the humanities are passing through a critical period of transformation. There is a growing interest in semiotics and semiotic philosophy in many areas of the humanities. Such a case, on which we draw, is the development of a theoretical semiotic approach to education, namely edusemiotics (Stables and Semetsky, Pedagogy and edusemiotics: theoretical challenge/practical opportunities, Sense Publishers, Rotterdam, 2015).

Exploring the role the brand plays in the choice of charity by UK volunteers

Charities need to understand why volunteers choose one brand rather than another in order to attract more volunteers to their organisation. There has been considerable academic interest in understanding why people volunteer generally. However, this research explores the more specific question of why a volunteer chooses one charity brand rather than another. It builds on previous conceptualisations of volunteering as a consumption decision. Seen through the lens of the individual volunteer, it considers the under-researched area of the decision-making process. The research adopts an interpretivist epistemology and subjectivist ontology. Qualitative data was collected through depth interviews and analysed using both Means-End Chain (MEC) and Framework Analysis methodology. The primary contribution of the research is to theory: understanding the role of brand in the volunteer decision-making process. It identifies two roles for brand. The first is as a specific reason for choice, an ‘attribute’ of the decision. Through MEC, volunteering for a well-known brand connects directly through to a sense of self, both self-respect but also social recognition by others. All four components of the symbolic consumption construct are found in the data: volunteers choose a well-known brand to say something about themselves. The brand brings credibility and reassurance, it reduces the risk and enables the volunteer to meet their need to make a difference and achieve a sense of accomplishment. The second closely related role for brand is within the process of making the volunteering decision. Volunteers built up knowledge about the charity brands from a variety of brand touchpoints, over time. At the point of decision-making that brand knowledge and engagement becomes relevant, enabling some to make an automatic choice despite the significant level of commitment being made. The research identifies four types of decision-making behaviour. The research also makes secondary contributions to MEC methodology and to the non-profit context. It concludes within practical implications for management practice and a rich agenda for future research.

Cellular and molecular characterization of an embryonic cell line (BME26) from the tick Rhipicephalus (Boophilus) microplus

The cellular and molecular characteristics of a cell line (BME26) derived from embryos of the cattle tick Rhipicephalus (Boophilus) microplus were studied. The cells contained glycogen inclusions, numerous mitochondria, and vesicles with heterogeneous electron densities dispersed throughout the cytoplasm. Vesicles contained lipids and sequestered palladium meso-porphyrin (Pd-mP) and rhodamine-hemoglobin, suggesting their involvement in the autophagic and endocytic pathways. The cells phagocytosed yeast and expressed genes encoding the antimicrobial peptides (microplusin and defensin). A cDNA library was made and 898 unique mRNA sequences were obtained. Among them, 556 sequences were not significantly similar to any sequence found in public databases. Annotation using Gene Ontology revealed transcripts related to several different functional classes. We identified transcripts involved in immune response such as ferritin, serine proteases, protease inhibitors,. antimicrobial peptides, heat shock protein, glutathione S-transferase, peroxidase, and NADPH oxidase. BME26 cells transfected with a plasmid carrying a red fluorescent protein reporter gene (DsRed2) transiently expressed DsRed2 for up to 5 weeks. We conclude that BME26 can be used to experimentally analyze diverse biological processes that occur in R. (B.) microplus such as the innate immune response to tick-borne pathogens. (C) 2008 Elsevier Ltd. All rights reserved.

TOWARD SEMANTIC WEB SERVICES AS MVC APPLICATIONS: FROM OWL-S VIA UML

OWL-S is an application of OWL, the Web Ontology Language, that describes the semantics of Web Services so that their discovery, selection, invocation and composition can be automated. The research literature reports the use of UML diagrams for the automatic generation of Semantic Web Service descriptions in OWL-S. This paper demonstrates a higher level of automation by generating complete complete Web applications from OWL-S descriptions that have themselves been generated from UML. Previously, we proposed an approach for processing OWL-S descriptions in order to produce MVC-based skeletons for Web applications. The OWL-S ontology undergoes a series of transformations in order to generate a Model-View-Controller application implemented by a combination of Java Beans, JSP, and Servlets code, respectively. In this paper, we show in detail the documents produced at each processing step. We highlight the connections between OWL-S specifications and executable code in the various Java dialects and show the Web interfaces that result from this process.

The CATH Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., alpha beta-motifs, alpha-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous.

The Aedes aegypti larval transcriptome: a comparative perspective with emphasis on trypsins and the domain structure of peritrophins

The genome sequence of Aedes aegypti was recently reported. A significant amount of Expressed Sequence Tags (ESTs) were sequenced to aid in the gene prediction process. In the present work we describe an integrated analysis of the genomic and EST data, focusing on genes with preferential expression in larvae (LG), adults (AG) and in both stages (SG). A total of 913 genes (5.4% of the transcript complement) are LG, including ion transporters and cuticle proteins that are important for ion homeostasis and defense. From a starting set of 245 genes encoding the trypsin domain, we identified 66 putative LG, AG, and SG trypsins by manual curation. Phylogenetic analyses showed that AG trypsins are divergent from their larval counterparts (LG), grouping with blood-induced trypsins from Anopheles gambiae and Simulium vittatum. These results support the hypothesis that blood-feeding arose only once, in the ancestral Culicomorpha. Peritrophins are proteins that interlock chitin fibrils to form the peritrophic membrane (PM) that compartmentalizes the food in the midgut. These proteins are recognized by having chitin-binding domains with 6 conserved Cys and may also present mucin-like domains (regions expected to be highly O-glycosylated). PM may be formed by a ring of cells (type 2, seen in Ae. aegypti larvae and Drosophila melanogaster) or by most midgut cells (type 1, found in Ae. aegypti adult and Tribolium castaneum). LG and D. melanogaster peritrophins have more complex domain structures than AG and T. castaneum peritrophins. Furthermore, mucin-like domains of peritrophins from T. castaneum (feeding on rough food) are lengthier than those of adult Ae. aegypti (blood-feeding). This suggests, for the first time, that type 1 and type 2 PM may have variable molecular architectures determined by different peritrophins and/or ancillary proteins, which may be partly modulated by diet.

Screening the Schistosoma mansoni transcriptome for genes differentially expressed in the schistosomulum stage in search for vaccine candidates

Schistosomiasis affects more than 200 million people worldwide; another 600 million are at risk of infection. The schistosomulum stage is believed to be the target of protective immunity in the attenuated cercaria vaccine model. In an attempt to identify genes up-regulated in the schistosomulum stage in relation to cercaria, we explored the Schistosoma mansoni transcriptome by looking at the relative frequency of reads in EST libraries from both stages. The 400 genes potentially up-regulated in schistosomula were analyzed as to their Gene Ontology categorization, and we have focused on those encoding-predicted proteins with no similarity to proteins of other organisms, assuming they could be parasite-specific proteins important for survival in the host. Up-regulation in schistosomulum relative to cercaria was validated with real-time reverse transcription polymerase chain reaction (RT-PCR) for five out of nine selected genes (56%). We tested their protective potential in mice through immunization with DNA vaccines followed by a parasite challenge. Worm burden reductions of 16-17% were observed for one of them, indicating its protective potential. Our results demonstrate the value and caveats of using stage-associated frequency of ESTs as an indication of differential expression coupled to DNA vaccine screening in the identification of novel proteins to be further investigated as potential vaccine candidates.

A Harmonized Vocabulary For Water Quality

Interoperability of water quality data depends on the use of common models, schemas and vocabularies. However, terms are usually collected during different activities and projects in isolation of one another, resulting in vocabularies that have the same scope being represented with different terms, using different formats and formalisms, and published in various access methods. Significantly, most water quality vocabularies conflate multiple concepts in a single term, e.g. quantity kind, units of measure, substance or taxon, medium and procedure. This bundles information associated with separate elements from the OGC Observations and Measurements (O&M) model into a single slot. We have developed a water quality vocabulary, formalized using RDF, and published as Linked Data. The terms were extracted from existing water quality vocabularies. The observable property model is inspired by O&M but aligned with existing ontologies. The core is an OWL ontology that extends the QUDT ontology for Unit and QuantityKind definitions. We add classes to generalize the QuantityKind model, and properties for explicit description of the conflated concepts. The key elements are defined to be sub-classes or sub-properties of SKOS elements, which enables a SKOS view to be published through standard vocabulary APIs, alongside the full view. QUDT terms are re-used where possible, supplemented with additional Unit and QuantityKind entries required for water quality. Along with items from separate vocabularies developed for objects, media, and procedures, these are linked into definitions in the actual observable property vocabulary. Definitions of objects related to chemical substances are linked to items from the Chemical Entities of Biological Interest (ChEBI) ontology. Mappings to other vocabularies, such as DBPedia, are in separately maintained files. By formalizing the model for observable properties, and clearly labelling the separate concerns, water quality observations from different sources may be more easily merged and also transformed to O&M for cross-domain applications.

Harmonization Of Vocabularies For Water Data

Observational data encodes values of properties associated with a feature of interest, estimated by a specified procedure. For water the properties are physical parameters like level, volume, flow and pressure, and concentrations and counts of chemicals, substances and organisms. Water property vocabularies have been assembled at project, agency and jurisdictional level. Organizations such as EPA, USGS, CEH, GA and BoM maintain vocabularies for internal use, and may make them available externally as text files. BODC and MMI have harvested many water vocabularies alongside others of interest in their domain, formalized the content using SKOS, and published them through web interfaces. Scope is highly variable both within and between vocabularies. Individual items may conflate multiple concerns (e.g. property, instrument, statistical procedure, units). There is significant duplication between vocabularies. Semantic web technologies provide the opportunity both to publish vocabularies more effectively, and achieve harmonization to support greater interoperability between datasets. - Models for vocabulary items (property, substance/taxon, process, unit-of-measure, etc) may be formalized OWL ontologies, supporting semantic relations between items in related vocabularies; - By specializing the ontology elements from SKOS concepts and properties, diverse vocabularies may be published through a common interface; - Properties from standard vocabularies (e.g. OWL, SKOS, PROV-O and VAEM) support mappings between vocabularies having a similar scope - Existing items from various sources may be assembled into new virtual vocabularies However, there are a number of challenges: - use of standard properties such as sameAs/exactMatch/equivalentClass require reasoning support; - items have been conceptualised as both classes and individuals, complicating the mapping mechanics; - re-use of items across vocabularies may conflict with expectations concerning URI patterns; - versioning complicates cross-references and re-use. This presentation will discuss ways to harness semantic web technologies to publish harmonized vocabularies, and will summarise how many of the challenges may be addressed.

Ontologia para moelos de negócios de redes sociais na internet: um ensaio teórico-exploratório

Atualmente, uma profusão de soluções chamadas de Web 2.0 e redes sociais está causando um grande impacto no desenvolvimento da Internet, comparando-se à era “ponto-com” em termos de crescimento, investimentos e empolgação. Estas iniciativas possuem em comum um elevado grau de formação de comunidades, e de criação e compartilhamento de conteúdo por parte do usuário, dentre outras características. Acredita-se que as redes sociais possuam um grande potencial inovador e disruptivo tanto para a sociedade quanto para o mundo empresarial. Entretanto, como transformar as redes sociais e aplicações Web 2.0 em modelos de negócios auto-sustentáveis ainda é um desafio para o mercado. Esta dissertação objetiva auxiliar a compreensão e abordagem deste tema propondo uma ontologia específica para modelos de negócios de redes sociais na internet. Isto se realiza por meio do desenvolvimento de um ensaio teórico de viés exploratório, baseado em extensa, porém não exaustiva, revisão de literatura abordando modelos de negócios, redes sociais e demais temas relacionados. A ontologia criada é então aplicada na representação de modelos de negócio de redes sociais na internet. Este trabalho também fornece uma visão geral do fenômeno Web 2.0, abordando algumas de suas principais características tecnológicas e socioeconômicas.

O sindicalismo e a administração publica

A dissertação aqui apresentada versa sobre uma temática nova, quer vista sob a ótica do nascimento do fato sociológico analisado - O Sindicalismo e a Administração Pública quer se considere a quase inexistência de fontes nas quais se possa abeberar, para que fosse possível estabelecer o fio condutor no desenvolvimento do tema. A temática foi analisada em dois planos: primeiro, fêz-se uma apreciação crítica da história do associativismo no Brasil, em sua simbiose com o aspecto social, com o lado econômico e com o lastro jurídico, ao ser analisado o caminho percorrido desde o primeiro clarão do Brasil até os dias presentes. Em segundo estágio, perquiriu-se a questão sindical, no que diz respeito à sua etiologia, o seu despertar mais consciente na década de 80 do nosso século, perpassando pela criação das Centrais Sindicais, ao serem detectados os desvios ideológicos, as contradições, a sua fisiologia em função de sua organização, ideário e ação na direção do que se propõem em nome de seus afiliados. Com efeito, o núcleo do trabalho se cinge à arregimentação do corpo de funcionários públicos com vistas a um eficaz - hoje, ainda muito incipiente - congraçamento, ao se deparar com uma forte resistência institucional, de vez que só a partir da Constituição de 1988, é que se abriu caminho para o direito de associação sindical a esse estamento dos agentes públicos. As disfunções são, aí, analisadas em relação ao despreparo dos Recursos Humanos no exercício de liderança e em confronto com a estrutura institucional anacrônica e de feitio autoritário, para fazer valer, de forma eficaz e efetiva, um bom desempenho da ação sindical, que se deseja genuína, autônoma e autógena, em função dos interesses de classe e a ter em vista a excelência dos serviços públicos; o fenômeno estudado, inversamente, mostra o processamento de uma luta sindical radicada em estrutura antidemocrática, em que o Estado financia os sindicatos e todo o aparelhamento sindical vertical, via contribuição sindical e a considerar que esse lastro sustentador da luta sindical é decalque de uma época de predominância de valores chauvinistas, exaltados no Brasil - e em outros países -, nas décadas de 30 e 40. Ainda foi feito um estudo comparativo com três modelos de sindicalismo, quais sejam: o francês, o alemão e o português. Os dois primeiros por razões de se constituirem em paradigmas de países centrais, tendo em vista que: (1) a França é modelo inspirador das instituições ocidentais, em sede político-jurídico-social, haja vista a sua História prenhe de fatos solapadores do statu quo ante; e (2) a Alemanha, por ter uma classe eficazmente institucionalizada de agentes públicos, tendo tradição araigada desde a burocracia prussiana, o que dá o toque de elevado profissionalismo a esses agentes públicos, os quais contam com uma agremiação sindical que guarda independência com relação ao movimento sindical do trabalhador privado, este, também consolidado em poderosa organização sindical naquele país. Portugal aparece no trabalho como o ascendente cultural do Brasil, o que implica em ser mostrado o nascedouro sindical desse país, dentro do clima cultural em que viveu e vive a península lusitana, e com isso se tenta elucidar o estágio de seu sindicalismo, as suas disfunções e auto funções , as suas semelhanças com o modelo brasileiro, as suas inclinações e natureza. As conclusões aferidas registram alguns aspectos relevantes: 1º) o Brasil nasceu de uma Administração centralizadora, marcada por uma máquina administrativa ineficaz, ineficiente, com a marca do Estato-império e sem a presença da construção concomitante de uma nação que é retardatária no assentar a viga da cidadania, o que levou a delongar a formação dos anseios e do espírito genuinamente autóctones. A repressão ao desenvolvimento das letras foi um entrave à criação de um espírito de povo, com a variante de ser uma maioria inculta, massacrantemente iletrada, em meio a uma pirâmide social em que se registrava apenas uma base desmesurada e um vértice acanhado, sem ter de permeio outras classes sociais que pudessem ser ou vir a ser estratificadas. Na esteira desses elementos, concluiu-se que: 2º) o movimento associativo é uma realidade incipiente e adormecido durante séculos, o que desbordou em uma apatia que só hoje começa a ser sacudida, através dos movimentos associativistas e sindical, este último nascido no meio das fábricas e estendido a algumas capitais de maior relevância política ou de maior peso econômico. o aspecto de maior magnitude para o trabalho foi a sinalização aberta aos servidores públicos para que se sindicalizassem, do que decorreu a conclusão de que essa ação precisa ser tangenciada e carreada a ser um movimento mais autenticamente ligado aos interesses da classe, pois por desvirtuamento contingencial em face da iniciante pouca expressão e inexperiência desse estamento, a ação sindical desses servidores sempre esteve à ilharga do movimento sindical do trabalhador privado, o qual tem outra linha de ação direcionada a interesses mais ligados ao conflito trabalho vs. capital, interesses esses que não se coadunam e nem se identificam com as aspirações e necessidades do funcionalismo público, mesmo que, muitas vezes, a questão do conflito desses agentes tenha uma interface no conjunto da pauta de reivindicação dos trabalhadores privados, ou seja, a questão salarial. O imperativo maior - e esta é a base da recomendação mais substancial - é conduzir a ação dos agentes públicos de forma heterodoxa na direção de se independentizar o movimento sindical desses agentes, a ser impulsionado pelas suas peculiaridades e por sua essencialidade ditada pela sua ontologia de servidores da coisa pública e tendo o público como sua clientela. Este é, em síntese, o caminho aqui trilhado.

OpenWordNet-PT: an open brazilian wordnet for reasoning

Brazilian Portuguese needs a Wordnet that is open access, downloadable and changeable, so that it can be improved by the community interested in using it for knowledge representation and automated deduction. This kind of resource is also very valuable to linguists and computer scientists interested in extracting and representing knowledge obtained from texts. We discuss briefly the reasons for a Brazilian Portuguese Wordnet and the process we used to get a preliminary version of such a resource. Then we discuss possible steps to improving our preliminary version.

Supply chain turbulence: the impact of a mid-range event in multi-tier, multi-dimension supply chains

Nota: A autora agradece à Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) pela concessão de bolsa de estudos para o desenvolvimento deste projeto de pesquisa.