Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

Many of the important changes in evolution are regulatory in nature. Sequenced bacterial genomes point to flexibility in regulatory circuits but we do not know how regulation is remodeled in evolving bacteria. Here, we study the regulatory changes that emerge in populations evolving under controlled conditions during experimental evolution of Escherichia coli in a phosphate-limited chemostat culture. Genomes were sequenced from five clones with different combinations of phenotypic properties that coexisted in a population after 37 days. Each of the distinct isolates contained a different mutation in 1 of 3 highly pleiotropic regulatory genes (hfq, spoT, or rpoS). The mutations resulted in dissimilar proteomic changes, consistent with the documented effects of hfq, spoT, and rpoS mutations. The different mutations do share a common benefit, however, in that the mutations each redirect cellular resources away from stress responses that are redundant in a constant selection environment. The hfq mutation lowers several individual stress responses as well the small RNA-dependent activation of rpoS translation and hence general stress resistance. The spoT mutation reduces ppGpp levels, decreasing the stringent response as well as rpoS expression. The mutations in and upstream of rpoS resulted in partial or complete loss of general stress resistance. Our observations suggest that the degeneracy at the core of bacterial stress regulation provides alternative solutions to a common evolutionary challenge. These results can explain phenotypic divergence in a constant environment and also how evolutionary jumps and adaptive radiations involve altered gene regulation.

CD4(+) CD25(+) Foxp3(+) Regulatory T Cells, Dendritic Cells, and Circulating Cytokines in Uncomplicated Malaria: Do Different Parasite Species Elicit Similar Host Responses?

Clearing blood-stage malaria parasites without inducing major host pathology requires a finely tuned balance between pro- and anti-inflammatory responses. The interplay between regulatory T (Treg) cells and dendritic cells (DCs) is one of the key determinants of this balance. Although experimental models have revealed various patterns of Treg cell expansion, DC maturation, and cytokine production according to the infecting malaria parasite species, no studies have compared all of these parameters in human infections with Plasmodium falciparum and P. vivax in the same setting of endemicity. Here we show that during uncomplicated acute malaria, both species induced a significant expansion of CD4(+) CD25(+) Foxp3(+) Treg cells expressing the key immunomodulatory molecule CTLA-4 and a significant increase in the proportion of DCs that were plasmacytoid (CD123(+)), with a decrease in the myeloid/plasmacytoid DC ratio. These changes were proportional to parasite loads but correlated neither with the intensity of clinical symptoms nor with circulating cytokine levels. One-third of P. vivax-infected patients, but no P. falciparum-infected subjects, showed impaired maturation of circulating DCs, with low surface expression of CD86. Although vivax malaria patients overall had a less inflammatory cytokine response, with a higher interleukin-10 (IL-10)/tumor necrosis factor alpha (TNF-alpha) ratio, this finding did not translate to milder clinical manifestations than those of falciparum malaria patients. We discuss the potential implications of these findings for species-specific pathogenesis and longlasting protective immunity to malaria.

Deficiency of the human complement regulatory protein factor H associated with low levels of component C9

We identified a 4-year-old Brazilian boy from a family of Japanese descent and history of consanguinity, who suffered from severe recurrent pneumonia. He carries factor H (FH) deficiency associated with reduced levels of component C9 and low serum levels of C3 and factor B. His mother also presented low levels of these proteins and factor I, while his father and sister had only lower levels of FH. Western blot assays confirmed the complete absence of FH and FHL-1 polypeptides in this patient. Sequencing of the proband`s FH cDNA revealed a homozygous G453A substitution, encoding an Arg(127)His change. His mother, father and sister are heterozygous for this substitution. Despite the absence of FH in the plasma, this protein was detected in the patient`s fibroblasts, suggesting that Arg(127) may be important for FH secretion. Low concentrations of C9 were detected in the proband serum but no mutations in the patient`s C9 gene or promoter have been identified, suggesting that this is a consequence of uncontrolled complement activation and high C9 consumption.

Allogeneic apoptotic thymocyte-stimulated dendritic cells expand functional regulatory T cells

P>Dendritic cells (DCs) play an important role in the clearance of apoptotic cells. The removal of apoptotic cells leads to peripheral tolerance, although their role is still not clear. We show that the uptake of apoptotic thymocytes by DCs converts these cells into tolerogenic DCs resistant to maturation by lipopolysaccharide, modulating the production of interleukin-12 and up-regulating the expression of transforming growth factor-beta(1) latency associated peptide. We also observed that DCs pulsed with apoptotic cells in the allogeneic context were more efficient in the expansion of regulatory T cells (Tregs), and that this expansion requires contact between DCs and the T cell. The Tregs sorted from in vitro culture suppressed the proliferation of splenocytes in vitro in a specific and non-specific manner. In the in vivo model, the transfer of CD4+ CD25- cells to Nude mice induced autoimmunity, with cell infiltrate found in the stomach, colon, liver and kidneys. The co-transfer of CD4+ CD25- and CD4+ CD25+ prevented the presence of cell infiltrates in several organs and increased the total cell count in lymph nodes. Our data indicate that apoptotic cells have an important role in peripheral tolerance via induction of tolerogenic DCs and CD4+ CD25+ Foxp3+ cells that present regulatory functions.

Inferring Contagion in Regulatory Networks

Several gene regulatory network models containing concepts of directionality at the edges have been proposed. However, only a few reports have an interpretable definition of directionality. Here, differently from the standard causality concept defined by Pearl, we introduce the concept of contagion in order to infer directionality at the edges, i.e., asymmetries in gene expression dependences of regulatory networks. Moreover, we present a bootstrap algorithm in order to test the contagion concept. This technique was applied in simulated data and, also, in an actual large sample of biological data. Literature review has confirmed some genes identified by contagion as actually belonging to the TP53 pathway.

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein

The human protein Ki-1/57 was first identified through the cross reactivity of the anti-CD30 monoclonal antibody Ki-1; in Hodgkin lymphoma cells. The expression of Ki-1/57 in diverse cancer cells and its phosphorylation in peripheral blood leukocytes after mitogenic activation suggested its possible role in cell signaling. Ki-1/57 interacts with several other regulatory proteins involved in cellular signaling, transcriptional regulation and RNA metabolism, suggesting it may have pleiotropic functions. In a previous spectroscopic analysis, we observed a low content of secondary structure for Ki-1/57 constructs. Here, Circular dichroism experiments, in vitro RNA binding analysis, and limited proteolysis assays of recombinant Ki-1/57(122-413) and proteolysis assays of endogenous full length protein from human HEK293 cells suggested that Ki-1/57 has characteristics of an intrinsically unstructured protein. Small-angle X-ray scattering (SAXS) experiments were performed with the C-terminal fragment Ki-1/57(122-413). These results indicated an elongated shape and a partially unstructured conformation of the molecule in solution, confirming the characteristics of an intrinsically unstructured protein. Experimental curves together with ab initio modeling approaches revealed an extended and flexible molecule in solution. An elongated shape was also observed by analytical gel filtration. Furthermore, sedimentation velocity analysis suggested that Ki-1/57 is a highly asymmetric protein. These findings may explain the functional plasticity of Ki-1/57, as suggested by the wide array of proteins with which it is capable of interacting in yeast two-hybrid interaction assays.

Supervision as control system : the design of supervision as a regulatory instrument in the social services sector in Sweden

In this article, the prevailing official view of supervision as a regulatory instrument is examined as it applies to the social services sector in Sweden. The study is based on a comparison of the views expressed on the design of supervision as a regulatory instrument by two government commissions, the Supervision Commission and the Commission on Supervision within the Social Services (UTIS), and on the positions taken by the Government regarding the definitions of the concept of supervision proposed by these commissions. The view of supervision as a regulatory instrument expressed in these policy documents is analysed with the help of a theoretical framework describing the components, their functions and the governance characteristics of control systems. In the framework separate interrelated characteristics of the components are identified and summarized into two models of control systems. The analysis shows that supervision in the Swedish social services sector can be described in terms of both a disciplinary and non-disciplinary system. By its system theoretical basis and the identification of interrelated characteristics the study contributes to a broadened understanding of the construction and functions of supervision as a regulatory instrument and of how supervision within the Swedish social sector is meant to be designed.

'In Charge of the Truffula Seeds' : On Children's Literature, Rationality and Children's Voices in Philosophy

In this paper I investigate how philosophy can speak for children and how children can have a voice in philosophy and speak for philosophy. I argue that we should understand children as responsible rational individuals who are involved in their own philosophical inquiries and who can be involved in our own philosophical investigations-not because of their rational abilities, but because we acknowledge them as conversational partners, acknowledge their reasons as reasons, and speak for them as well as let them speak for us and our rational community. In order to argue this I turn, first, to Gareth Matthews' philosophy of childhood and suggest a reconstruction of some of his concepts in line with the philosophy of Stanley Cavell. Second, in order to examine more closely our conceptions of rationality and our pictures of children, I consider the children's books, The Lorax and Where is My Sister? and Henrik Ibsen's play, The Wild Duck.

Brazil's regulatory framework: predictability or uncertainty?

Este Trabalho Discute as Perspectivas da Regulação Econômica no Brasil. para Tanto, Primeiramente Apresenta-Se a Evolução Histórica da Regulação no País, Discutindo as Principais Questões Relacionadas Às Agências Reguladoras Federais. em Segundo Lugar, os Marcos Regulatórios de Cinco Diferentes Setores (Telecomunicações, Eletricidade, Saneamento Básico, Petróleo e Gás Natural) são Analisados. em Terceiro Lugar, a Questão do Financiamento de Investimentos em Infra-Estrutura é Tratada, Enfatizando o Papel das Parcerias Público-Privadas (Ppps). uma Seção Final Cont~Em um Possível Agenda para a Regulação no Brasil

Um desafio para a regulação do mercado de assistência à saúde no Brasil: a escolha do consumidor de planos de saúde

The objective of this dissertation is to discover and to analyze the way how the consumer uses his/her perception to decide contracting a health plan, to supply elements that can serve to subsidize the State, the market and the consumers, in relation to the knowledge on the process of choice of the consumer and the decisions of purchase and contracting services of private health. The estimated one is to evidence that the brand of health plan is an important variable and decisive to the consumer contracting the service of a company that operates in these sector, because mean for the consumer security about the product, through the symbolism that the same one represents, despite the consumer not knowing to the certainty what is contracting in quality and amount. The theoretical construction is carried through using literature of anthropology of the consumption, theory of modernity, theory of the regulation, economic utilitarism, and marketing. Moreover, referential specific theoretician on the regulation of the market of health plans in Brazil. The health plan market in Brazil is anti-symmetrical and the consumer doesn¿t have knowledge technician who makes possible it to form judgment and to carry through rationality choices. Than the consumer uses to his/her decision symbolic elements that are available to his/her and supply to his/her the security that is look likes in the consumption of this kind of good. These symbolic elements related the confidence and security and are into the strong brands of the companies and are transmitted to the consumer through the mass media. In this dissertation are used as sources of data some information of the regulatory agency of the sector ¿ ANS -, a research of public opinion with health plans users and the results of the application of proper questionnaires for this research.