Phylum-wide transcriptome analysis of oogenesis and early embryogenesis in selected nematode species

Oogenesis is a prerequisite for embryogenesis in Metazoa. During both biological processes important decisions must be made to form the embryo and hence ensure the next generation: (1) Maternal gene products (mRNAs, proteins and nutrients) must be supplied to the embryo. (2) Polarity must be established and axes must be specified. While incorporation of maternal gene products occurs during oogenesis, the time point of polarity establishment and axis specification varies among species, as it is accomplished either prior, during, or after fertilisation. But not only the time point when these events take place varies among species but also the underlying mechanisms by which they are triggered. For the nematode model Caenorhabditis elegans the underlying pathways and gene regulatory networks (GRNs) are well understood. It is known that there the sperm entry point initiates a primary polarity in the 1-celled egg and with it the establishment of the anteroposterior axis. However, studies of other nematodes demonstrated that polarity establishment can be independent of sperm entry (Goldstein et al., 1998; Lahl et al., 2006) and that cleavage patterns, symmetry formation and cell specification also differ from C. elegans. In contrast to the studied Chromadorea (more derived nematodes including C. elegans), embryos of some marine Enoplea (more basal representatives) even show no discernible early polarity and blastomeres can adopt variable cell fates (Voronov and Panchin 1998). The underlying pathways controlling the obviously variant embryonic processes in non-Caenorhabditis nematodes are essentially unknown. In this thesis I addressed this issue by performing a detailed unbiased comparative transcriptome analysis based on microarrays and RNA sequencing of selected developmental stages in a variety of nematodes from different phylogenetic branches with C. elegans as a reference system and a nematomorph as an outgroup representative. In addition, I made use of available genomic data to determine the presence or absence of genes for which no expression had been detected. In particular, I focussed on components of selected pathways or GRNs which are known to play essential roles during C. elegans development and/or other invertebrate or vertebrate model systems. Oogenesis must be regulated differently in non-Caenorhabditis nematodes, as crucial controlling components of Wnt and sex determination signaling are absent in these species. In this respect, I identified female-specific expression of potential polarity associated genes during gonad development and oogenesis in the Enoplean nematode Romanomermis culicivorax. I could show that known downstream components of the polarity complexes PAR-3/-6/PKC-3 and PAR-1/-2 are absent in non-Caenorhabditis species. Even PAR-2 as part of the polarity complex does not exist in these nematodes. Instead, transcriptomes of nematodes (including C. elegans), show expression of other polarity-associated complexes such as the Lgl (Lethal giant larvae) complex. This result could pose an alternative route for nematodes and nematomorphs to initiate polarity during early embryogenesis. I could show that crucial pathways of axis specification, such as Wnt and BMP are very different in C. elegans compared to other nematodes. In the former, Wnt signaling, for instance, is mediated by four paralogous beta-catenins, while other Chromadorea have fewer and Enoplea only one beta-catenin. The transcriptomes of R. culicivorax and the nematomorph show that regulators of BMP (e.g. Chordin), are specifically expressed during early embryogenesis only in Enoplea and the close outgroup of nematomorphs. In conclusion, my results demonstrate that the molecular machinery controlling oogenesis and embryogenesis in nematodes is unexpectedly variable and C. elegans cannot be taken as a general model for nematode development. Under this perspective, Enoplean nematodes show more similarities with outgroups than with C. elegans. It appears that certain pathway components were lost or gained during evolution and others adopted new functions. Based on my findings I can conjecture, which pathway components may be ancestral and which were newly acquired in the course of nematode evolution.

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to develop tools to evaluate risks for TB disease caused by M. bovis/M.caprae and for TB control in humans and animals.

O futebol que se aprende e o futebol que se ensina

Universidade Estadual de Campinas . Faculdade de Educação Física

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus

We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility ( het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer ( HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated ""gene dumps'' and, perhaps, simultaneously, as "" gene factories''.

New genes of Xanthomonas citri subsp citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library

Background: Citrus canker is a disease caused by the phytopathogens Xanthomonas citri subsp. citri, Xanthomonas fuscans subsp. aurantifolli and Xanthomonas alfalfae subsp. citrumelonis. The first of the three species, which causes citrus bacterial canker type A, is the most widely spread and severe, attacking all citrus species. In Brazil, this species is the most important, being found in practically all areas where citrus canker has been detected. Like most phytobacterioses, there is no efficient way to control citrus canker. Considering the importance of the disease worldwide, investigation is needed to accurately detect which genes are related to the pathogen-host adaptation process and which are associated with pathogenesis. Results: Through transposon insertion mutagenesis, 10,000 mutants of Xanthomonas citri subsp. citri strain 306 (Xcc) were obtained, and 3,300 were inoculated in Rangpur lime (Citrus limonia) leaves. Their ability to cause citrus canker was analyzed every 3 days until 21 days after inoculation; a set of 44 mutants showed altered virulence, with 8 presenting a complete loss of causing citrus canker symptoms. Sequencing of the insertion site in all 44 mutants revealed that 35 different ORFs were hit, since some ORFs were hit in more than one mutant, with mutants for the same ORF presenting the same phenotype. An analysis of these ORFs showed that some encoded genes were previously known as related to pathogenicity in phytobacteria and, more interestingly, revealed new genes never implicated with Xanthomonas pathogenicity before, including hypothetical ORFs. Among the 8 mutants with no canker symptoms are the hrpB4 and hrpX genes, two genes that belong to type III secretion system (TTSS), two hypothetical ORFS and, surprisingly, the htrA gene, a gene reported as involved with the virulence process in animal-pathogenic bacteria but not described as involved in phytobacteria virulence. Nucleic acid hybridization using labeled cDNA probes showed that some of the mutated genes are differentially expressed when the bacterium is grown in citrus leaves. Finally, comparative genomic analysis revealed that 5 mutated ORFs are in new putative pathogenicity islands. Conclusion: The identification of these new genes related with Xcc infection and virulence is a great step towards the understanding of plant-pathogen interactions and could allow the development of strategies to control citrus canker.

Análise econômica comparativa de empresas de água mineral quanto ao porte

This work makes a comparative economic analysis of a small-, medium- and large-sized mineral water company, the three of which are localized in the State of Sao Paulo. All have the same lines of production such as glasses, bottles and big bottles. The analysis involves the cash flow comparison of the three companies.

Evidence of caspase-mediated apoptosis induced by L-amino acid oxidase isolated from Bothrops atrox snake venom

The aim of this work was to investigate the involvement of caspases in apoptosis induced by L-amino acid oxidase isolated from Bothrops atrox snake venom. The isolation of LAAO involved three chromatographic steps: molecular exclusion on a G-75 column; ion exchange column by HPLC and affinity chromatography on a Lentil Lectin column. SDS-PAGE was used to confirm the expected high purity level of BatroxLAA0. It is a glycoprotein with 12% sugar and an acidic character, as confirmed by its amino acid composition, rich in ""Asp and Glu"" residues. It displays high specificity toward hydrophobic L-amino acids. The N-terminal amino acid sequence and internal peptide sequences showed close structural homology to other snake venom LAAOs. This enzyme induces in vitro platelet aggregation, which may be due to H(2)O(2) production by LAAOs, since the addition of catalase completely inhibited the aggregation effect. It also showed cytotoxicity towards several cancer cell lines: HL60, Jurkat, B16F10 and PC12. The cytotoxicity activity was abolished by catalase. A fluorescence microscopy evaluation revealed a significant increase in the apoptotic index of these cells after BatroxLAAO treatment. This observation was confirmed by phosphatidyl serine exposure and activation of caspases. BatroxLAAO is a protein with various biological functions that can be involved in envenomation. Further investigations of its function will contribute to toxicology advances. Published by Elsevier Inc.

Transport-Regional Equity Issue Revisited

Almeida E. S. de, Haddad E. A. and Hewings G. J. D. Transport-regional equity issue revisited, Regional Studies. The objective of this paper is to analyse the relationship between transport and regional equity in Minas Gerais, Brazil. Furthermore, the existence of a trade-off between economic performance and regional equity is investigated as well. To do so, the paper develops a spatial computable general equilibrium model based on Brocker and Schneider`s approach of 2002 to implement comparative static analysis, explicitly incorporating iceberg transportation costs. Four activities are modelled, namely production, final demand, transportation and exports. Two production factors are assumed: labour and other factors. The model has 12 domestic regions and three external regions. Four counterfactual experiments are developed based on decreases in transportation costs due to a `distance shortening`. The main findings indicate that if the transport infrastructure improvement is focused only among poor regions, the promotion of regional equity is insignificant. If the transport infrastructure improvement links are concentrated among rich regions, there is an increase in regional income inequalities. However, if the improvements are targeted to the roads linking poor regions and rich ones, there is greater promotion of regional equity. The same result will occur when improvements are made to all road links of the state. [image omitted] Almeida E. S. de, Haddad E. A. et Hewings G. J. D. La question du rapport entre le transport et l`equilibre regional vue sous un jour nouveau, Regional Studies. Cet article cherche a analyser le rapport entre le transport et l`equilibre regional en Minas Gerais au Bresil. En outre, on examine la presence d`un echange entre la performance economoique et l`equilibre regional. Pour le faire, on construit un modele geographique de l`equilibre general a utiliser sur ordinateur fonde sur l`approche de Brockner et Schneider en 2002 afin de mettre en oeuvre une analyse statique comparative qui comprend explicitement les frais de transport iceberg. On modelise quatre activites, a savoir, la production, la demande finale, le transport et l`exportation. On fait deux suppositions quant aux facteurs de production: la main-d`oevre et d`autres facteurs. Le modele embrasse douze regions internes et trois regions externes. On fait quatre experiences paradoxales fondees sur la baisse des frais de transport due a une `reduction des distances`. Les principaux resultats indiquent que si l`amelioration de l`equipement de transport ne porte que sur les regions defavorisees, la promotion de l`equilibre regional s`avere negligeable. Si l`amelioration de l`equipement de transport focalise les regions riches, il s`avere un creusement des ecarts des revenus regionaux. Cependant, si les ameliorations ciblent les routes qui relient les regions defavorisees aux regions riches, il s`avere une plus grande promotion de l`equilibre regional. Il en va de meme pour la situation ou on a apporte des amenagements a toutes les liaisons routieres de l`etat. Modele geographique de l`equilibre general a utiliser sur ordinateur Equilibre regional Peformance economique Frais de transport Almeida E. S. de, Haddad E. A. und Hewings G. J. D. Die Wiederaufnahme der Frage von Verkehrswesen im Verhaltnis zu regionaler Fairness, Regional Studies. Dieser Aufsatz beabsichtigt, die Beziehung zwischen Verkehrswesen und regionaler Fairness in Minas Gerais (Brasilien) zu analysieren und zugleich auch das Vorkommen von Einbussen entweder bei wirtschaftlicher Leistung der regionaler Fairness zu untersuchen. Zu diesem Zwecke wird ein auf dem Ansatz von Brocker und Schneider (2002) aufbauendes raumliches komputables allgemeines Gleichgewichtsmodell entwickelt, um vergleichende statistische Analysen durchzufuhren, wobei verborgene `Eisberg`-Transportkosten ausdrucklich berucksichtigt werden. Es werden vier Unternehmenstatigk eiten aufgefuhrt: Herstellung, Nachfrage, Transportwesen und Exporte, und zwei Produktionsfaktoren vorausgesetzt: Arbeitskrafte und andere Faktoren. Das Modell umfasst zwolf Inlandsregionen und drei externe Regionen. Es werden vier gegensatzliche Experimente entwickelt, die auf einer Abnahme der Transportkosten infolge einer `Verkurzung der Entfernungen` beruhen. Die Hauptbefunde weisen darauf hin, dass die Forderung regionaler Fairness unbedeutend bleibt, wenn die Verbesserungen der Transportinfrastruktur sich nur auf minderbemittelte Regionen konzentrieren; werden die Verbesserungen der Verbindungen der Transportinfrastruktur in wohlhabenden Regionen durchgefuhrt, so nehmen regionale Einkommensunterschiede zu. Wenn die Verbesserungen jedoch auf Strassen abzielen, die wohlhabende Regionen mit weniger bemittelten verbinden, wird regionale Fairness starker gefordert. Das gleiche Ergebnis wird sich einstellen, wenn Verbesserungen an allen Strassenverbindungen des Staates vorgenommen werden. Raumliches, komputables, allgemeines Gleichgewichtsmodell Regionale Fairness Wirtschaftsleistung Transportkosten Almeida E. S. de, Haddad E. A. y Hewings G. J. D. Revisando el tema de la igualdad del transporte en las regiones, Regional Studies. El objetivo de este documento es analizar la relacion entre el transporte y la igualdad regional en Minas Gerais, Brasil. Asimismo investigamos la existencia de una compensacion entre el rendimiento economico y la igualdad regional. Para ello desarrollamos un modelo de equilibrio general computable y espacial basado en el enfoque de Brocker y Schneider en 2002 para hacer un analisis estatico y comparativo, explicitamente incorporando los costes ocultos de transporte. Se modelan cuatro actividades: la produccion, la demanda final, el transporte y las exportaciones. Suponemos que existen dos factores de produccion: mano de obra y otros factores. En este modelo, existen doce regiones internas y tres regiones externas. Desarrollamos cuatro experimentos contrafactuales basados en la disminucion de los costes de transporte debido a una `acortamiento de las distancias`. Los principales resultados indican que si la mejora de la infraestructura del transporte se centra solo entre las regiones mas pobres, el fomento de la igualdad regional es insignificante. Si los enlaces de la mejora de la infraestructura del transporte se concentran en las regiones ricas, aumentan las desigualdades de ingresos regionales. Sin embargo, si se mejoran los enlaces de carreteras entre las regiones pobres y ricas, se fomenta mejor la igualdad regional. El mismo resultado ocurre cuando se mejoran los enlaces de todas las carreteras del estado. Modelo de equilibrio general computable y espacial Igualdad regional Rendimiento economico Costes de transporte.

Transforming the architect: Ownership form and archetype change

The adoption of the incorporated form of ownership in preference to partnership is linked to the shift to a more modem organizational archetype in professional firms. Yet existing empirical research offers insufficient insight into the organizational processes of this transformation in different professional arenas. Where ownership and control become separated, there is a clearer theoretical explanation of the implications for the way the firm is run. Where ownership and control remain inside, the firm, however, the consequences are not so clear and have not been well explored. Using survey and interview materials derived from a study of architecture practices, we examine the processes by which differences based on ownership emerge. Then, by drawing on Weberian theories, where they are concerned with professionalization as a project with material and social rewards, we specify more clearly the context for change in professional firms' archetypes. This, we conclude, provides a stronger basis for understanding the change trajectories of firms within professions and comparative organizational analysis between professions.

Dimensionamento à punção em apoios internos de lajes protendidas sem aderência

Esta dissertação trata da punção em lajes protendidas com cordoalhas não aderentes, para pilares internos, calculadas através das normas ABNT NBR 6118:2007, ABNT NBR 6118:2014, EN 1992-1-1:2004 e ACI 318-11. Ao longo do trabalho, são apresentados dimensionamentos à punção através desses códigos a fim de se obter uma análise comparativa dos resultados. Além disso, são expostas três situações de provas de carga não destrutivas para punção, realizadas em lajes reais. Os casos, verificados a partir da comparação entre as quatro normas, servem de base para avaliações sobre o nível de segurança estrutural entre os dimensionamentos. Após as análises teóricas, conclui-se que, no geral, o EC2:2004 e a NBR 6118:2014 são os códigos que geram os resultados menos conservadores no cálculo das armaduras de punção. Já o ACI 318-11 e a NBR 6118:2007 obtêm os resultados mais conservadores para esse dimensionamento. Quando considerados os carregamentos máximos sem utilização de armadura de punção, a norma americana se destaca, obtendo valores comparáveis aos do EC2:2004 e da NBR 6118:2014. A NBR 6118:2007 resulta em dimensionamentos sempre mais conservadores.

An integrated system to support electricity tariff contract definition

This paper presents an integrated system that helps both retail companies and electricity consumers on the definition of the best retail contracts and tariffs. This integrated system is composed by a Decision Support System (DSS) based on a Consumer Characterization Framework (CCF). The CCF is based on data mining techniques, applied to obtain useful knowledge about electricity consumers from large amounts of consumption data. This knowledge is acquired following an innovative and systematic approach able to identify different consumers’ classes, represented by a load profile, and its characterization using decision trees. The framework generates inputs to use in the knowledge base and in the database of the DSS. The rule sets derived from the decision trees are integrated in the knowledge base of the DSS. The load profiles together with the information about contracts and electricity prices form the database of the DSS. This DSS is able to perform the classification of different consumers, present its load profile and test different electricity tariffs and contracts. The final outputs of the DSS are a comparative economic analysis between different contracts and advice about the most economic contract to each consumer class. The presentation of the DSS is completed with an application example using a real data base of consumers from the Portuguese distribution company.

O casamento real de William e Kate : a cobertura jornalística nos jornais The Daily Mail, The Guardian e The Sun

Dissertação apresentada à Escola Superior de Comunicação Social como parte dos requisitos para obtenção de grau de mestre em Jornalismo.

Licensing endogenous cost-reduction in a differentiated Stackelberg model

In this paper we consider a differentiated Stackelberg model, when the leader firm engages in an R&D process that gives an endogenous cost-reducing innovation. The aim is to study the licensing of the cost-reduction by a two-part tariff. By using comparative static analysis, we conclude that the degree of the differentiation of the goods plays an important role in the results. We also do a direct comparison between our model and Cournot duopoly model.

Avaliação da função ventricular esquerda por ecocardiografia bidimensional com VVI em indivíduos hipertensos voluntários

Mestrado em Tecnologia de Diagnóstico e Intervenção Cardiovascular - Ramo de especialização: Ultrassonografia Cardiovascular

Os impostos especiais de consumo: instrumento de mercado interno ou criação de justiça tributária?

Mestrado em Fiscalidade