Interfacing cellular networks of <i>S. cerevisiae</i> and <i>E. coli</i>: Connecting dynamic and genetic information

BACKGROUND: In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote organisms. Still, the relation and the biological overlap among phenomenological and inferential gene networks, e.g., between the protein interaction network and the gene regulatory network inferred from large-scale transcriptomic data, is largely unexplored. RESULTS: We provide in this study an in-depth analysis of the structural, functional and chromosomal relationship between a protein-protein network, a transcriptional regulatory network and an inferred gene regulatory network, for S. cerevisiae and E. coli. Further, we study global and local aspects of these networks and their biological information overlap by comparing, e.g., the functional co-occurrence of Gene Ontology terms by exploiting the available interaction structure among the genes. CONCLUSIONS: Although the individual networks represent different levels of cellular interactions with global structural and functional dissimilarities, we observe crucial functions of their network interfaces for the assembly of protein complexes, proteolysis, transcription, translation, metabolic and regulatory interactions. Overall, our results shed light on the integrability of these networks and their interfacing biological processes

Age and habitat quality matters: isotopic variation of two sympatric species of rodents in Neotropical Forest

Dietary studies allow us to understand important ecological patterns such as intra- and interpopulation variation and interspecific differences regarding the use of food sources. Stable isotopes have been successfully employed to detect dietary differences between species and feeding shifts within a species, as a response to age, habitat use, and resource availability. Here we investigated the stable isotope compositions of carbon and nitrogen of young and adult specimens of Euryoryzomys russatus and Sooretamys angouya and their stomach contents, in a complex mosaic of vegetation in the Brazilian Atlantic Forest. Isotopes indicated a pronounced inter- and intraspecific plasticity in resource use for E. russatus and S. angouya. Plant sources were the prevalent feeding items for E. russatus, with low to intermediate consumption of arthropods. For S. angouya, plants were dominant in the stomach content, but arthropod arose as an important source. E. russatus showed more variation in isotopic signature between grids than S. angouya, suggesting that the former was more affected by habitat changes. These results allow us to better understand the ontogeny, diet and the behavioral responses to environmental variations of both species. Finally, our study contributes to reduce the lack of knowledge about sympatric species ecology and aggregates information for their conservation.Fil: Bovendorp, Ricardo Siqueira. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; Brasil. Universidade Estadual Paulista “Júlio de Mesquita Filho”; BrasilFil: Simoes Libardi, Gustavo. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Sarmento, Mariana Montagner de Moraes. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; BrasilFil: Camargo, Plínio Barbosa. Universidade de Sao Paulo; BrasilFil: Reis Percequillo, Alexandre. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz; Brasi

B-cell lymphoma gene regulatory networks: biological consistency among inference methods

Despite the development of numerous gene regulatory network (GRN) inference methods in the last years, their application, usage and the biological significance of the resulting GRN remains unclear for our general understanding of large-scale gene expression data in routine practice. In our study, we conduct a structural and a functional analysis of B-cell lymphoma GRNs that were inferred using 3 mutual information-based GRN inference methods: C3Net, BC3Net and Aracne. From a comparative analysis on the global level, we find that the inferred B-cell lymphoma GRNs show major differences. However, on the edge-level and the functional-level - that are more important for our biological understanding - the B-cell lymphoma GRNs were highly similar among each other. Also, the ranks of the degree centrality values and major hub genes in the inferred networks are highly conserved as well. Interestingly, the major hub genes of all GRNs are associated with the G-protein-coupled receptor pathway, cell-cell signaling and cell cycle. This implies that hub genes of the GRNs can be highly consistently inferred with C3Net, BC3Net and Aracne, representing prominent targets for signaling pathways. Finally, we describe the functional and structural relationship between C3Net, BC3Net and Aracne gene regulatory networks. Our study shows that these GRNs that are inferred from large-scale gene expression data are promising for the identification of novel candidate interactions and pathways that play a key role in the underlying mechanisms driving cancer hallmarks. Overall, our comparative analysis reveals that these GRNs inferred with considerably different inference methods contain large amounts of consistent, method independent, biological information

Species-specific evolving regions in the human and chimpanzee genomes

Vergleichende Genexpressionsanalysen zwischen Mensch und Schimpanse ermöglichen die Identifizierung von Kandidaten-Genen, die für die phänotypischen Unterschieden zwischen den beiden Arten verantwortlich sein können. Unterschiede in der Genexpression in frühen Stadien der Ontogenese spielen eine potentielle Schlüsselrolle bei der differentiellen Embryonalentwicklung der beiden Arten. Direkte Genexpressionsvergleiche in diesen Entwicklungsstadien sind allerdings in der Regel möglich, da embryonales Gewebe für solche Versuche weder vom Menschen noch vom Schimpansen zur Verfügung steht. In der vorliegenden Arbeit wird daher ein bioinformatischer Ansatz zur Identifizierung von Genen präsentiert, deren Expression sich in einer artspezifischen Weise verändert hat. Das Substitutionsmuster weist in transkribierten genomischen Regionen eine erhöhte Rate von A->G im Vergleich zu T->C Substitutionen auf, die auf den Effekt der transkriptions-gekoppelten Reparatur zurueckgeführt wird. Es wurden Gene im Genom von Mensch bzw. Schimpanse gesucht, deren Substitutionsmuster Anzeichen eines unterschiedlichen Ausmaßes an der transkription-gekoppelten Reparatur in den beiden Arten zeigen. Zunächst wurden spezifische Substitutionsmatrizen für 12,596 nicht-überlappende 125 Kb Alignmentfenster in der Fraktion des transkribierten Genoms für Mensch, Schimpansen und Rhesus geschätzt. Anschliessend wurde eine neue Teststatistik verwendet, mit der 717 transkribierte Genomregionen identifiziert wurden, bei denen sich die Substitutionsmatrizen von Mensch und Schimpanse signifikant unterscheiden. Die Substitutionsmatrizen unterscheiden sich hauptsächlich in ihrem relativen Ausmaß von AG im Vergleich zu TC Substitutionen. Genau ein solcher Unterschied ist zu erwarten, wenn die transkription-gekoppelte Reparatur im unterschiedlichem Maße auf die entsprechenden Gene der beiden Arten wirkt. Diese Beobachtung liefert erste Hinweise darauf, dass diese Gene während der fr\"uhen Stadien der Entwicklung von Mensch und Schimpanse differentiell exprimiert werden. Eine nachfolgende Genontologie Anreicherungsanalyse zeigt daß die entsprechenden Gene hauptsächlich eine Rolle in embryonalen Entwicklungsprozessen wie z.B. anatomische Strukturentwicklung (z.B. Skelett, Rückenmark, Gehirn, Darm), Neurogenese, Signaltransduktion, Transkriptionsregulation, Translation und Replikation spielen.Comparative analyses of the human and chimpanzee transcriptomes aim at the identification of genes whose expression pattern has changed since both species last shared a common ancestor. This approach complements the search for genes with altered function in compiling the catalogue of genetic changes responsible for the distinct phenotypes of the contemporary species. However, gene expression analyses are ultimately dependent on the availability of tissue samples. Embryonic tissues from chimpanzees are rare, if available at all. Thus, changes in the gene expression pattern in these early stages of ontogenesis, which potentially play a key role in differential development, are likely to be missed. Here I present a bioinformatics approach to identify candidates that may be expressed in a species-specific manner. Specifically, I have searched for genes in the human and chimpanzee genomes of which evolutionary sequence change shows signs of different extents of transcription-coupled-repair in the two species. Human, chimpanzee and rhesus branch-specific substitution matrices were estimated for 12,596 non-overlapping sliding windows 125 Kb in size representing the transcribed fraction in a human-chimpanzee-rhesus genome alignment. Applying a novel test statistic, 717 transcribed regions were identified in which the estimated branch-specific substitution models differ significantly between humans and chimpanzees. More specifically, it is shown that the two species differ mainly in their relative rates of AG and TC substitutions, and in the rate ratio of the two transition types. This pattern is expected when transcription-coupled-repair acts to different extents on the corresponding genes in the two species and provides initial evidence that these genes may be differentially expressed during early stages of human and chimpanzee development. A subsequent Gene Ontology enrichment analysis of the corresponding genes revealed an enrichment for embryonic developmental processes such as anatomical structure development (e.g., skeleton, spinal cord, brain, gut), neurogenesis, signal transduction and regulation processes for transcription, translation and replication

HOLISTIC WOMEN: "GREEN BLOUSE" NURSES TO THE SERVICE OF THE NATION

This study aims to investigate the role assigned to the holistic nurse and the education she receives to perform her role with maximum efficiency within the Brazilian Holistic Action (Acao Integralista Brasileira), a right-wing political party that emerged in Brazil in the 1930s. It uses holistic newspapers, the "Holistic Encyclopedia" collection, and records about the Holistic School of Nursing which compose the criminal collection by the Political Police, organized by the Special Police of Political and Social Safety as source material. As a result, the study presents a significant investment of holistic thinking in formally educating nurses, women who took the opportunity of the moment to expand their social arenas. It concludes that, although holistic thinking strengthened social roles described as female, the women's relationship with the movement was innovative because it enabled new practices and representations that they also started to develop in the public sphere, for example, working as nurses

First record of Calliactis tricolor (Le Sueur, 1817) (Cnidaria, Actiniaria, Hormathiidae) in the Veracruz reef system, southwestern Gulf of Mexico

The sea anemone Calliactis tricolor (Le Sueur, 1817) is an ecologically important member of the benthic community in coastal and coral reefs of the tropical Atlantic, particularly by their propensity to establish mutualistic symbiotic relationships with hermit crabs. This species is presumably distributed throughout the Gulf of Mexico; however, it had never been registered in the southwestern part of the Gulf. Here we document the first record of C. tricolor in two coral reef localities of the Veracruz Reef System, Mexico, and update the number of species of sea anemones known for the region.Fil: Tello Musi, José Luis. Universidad Nacional Autonoma de Mexico. Facultad de Estudios Superiores de Iztacala; MéxicoFil: González Muñoz, Ricardo Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Acuña, Fabian Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Simoes, Nuno. Universidad Nacional Autonoma de Mexico. Facultad de Ciencias; Méxic

Minas Gerais e o Brasil diante das opções de integração econômica

-Este projeto tem por objetivo construir um indicador de atividade econômica de alta freqüência, com periodicidade diária, para a cidade de Juiz de Fora a partir de dados de resíduos sólidos, coletados junto da Empresa Municipal Demlurb. Esse indicador preenche uma lacuna de índices de acompanhamento do desempenho econômico da cidade, com baixíssimo custo para a sua elaboração. A idéia desse índice baseia-se no fato de haver uma forte correlação positiva entre a produção de resíduos sólidos e a atividade econômica. Os resultados mostram que houve uma ligeira tendência de crescimento

The Atlas of Economic Complexity

Maps capture data expressing the economic complexity of countries from Albania to Zimbabwe, offering current economic measures and as well as a guide to achieving prosperity Why do some countries grow and others do not? The authors of The Atlas of Economic Complexity offer readers an explanation based on "Economic Complexity," a measure of a society's productive knowledge. Prosperous societies are those that have the knowledge to make a larger variety of more complex products.The Atlas of Economic Complexity attempts to measure the amount of productive knowledge countries hold and how they can move to accumulate more of it by making more complex products. Through the graphical representation of the "Product Space," the authors are able to identify each country's "adjacent possible," or potential new products, making it easier to find paths to economic diversification and growth. In addition, they argue that a country's economic complexity and its position in the product space are better predictors of economic growth than many other well-known development indicators, including measures of competitiveness, governance, finance, and schooling. Using innovative visualizations, the book locates each country in the product space, provides complexity and growth potential rankings for 128 countries, and offers individual country pages with detailed information about a country's current capabilities and its diversification options. The maps and visualizations included in the Atlas can be used to find more viable paths to greater productive knowledge and prosperity

Nursing students’ knowledge and attitudes toward older adults

Nursing students, as the future healthcare workforce, hold immense potential in providing quality care to older adults and becoming advocates for promoting aging and public health, thus contributing significantly to addressing the multifaceted challenges of our aging society. Nurses’ knowledge and attitudes about aging affect health care quality. Negative and unattractive representations of the social problems associated with aging contaminate nursing students’ attitudes. Nursing schools are challenged to develop new curricula to prepare future nurses for the inherent complexity of an aging society. This study aims to assess the knowledge and attitudes of nursing students toward older adults and identify the variables that can influence these attitudes. Quantitative research was carried out through the application of an online survey using a cross-sectional descriptive research design. A total of 182 nursing students completed the online survey. Progression in the nursing course was statistically significant; the more students advanced, the more positive attitudes and knowledge they revealed about aging; 39% of students have daily contact with their grandparents; however, only 14.8% would like to work with older adults. Multiple linear regression revealed that the most important factor for positive attitudes and knowledge about aging was regular contact with grandparents, followed by progression in the nursing course. The students’ age was not a significant factor in improving attitudes or expanding knowledge regarding older adults. In a multidimensional logic, the deepening of knowledge about aging and the socialization of students with older adults are central factors that should reinforce curricula in nursing education