Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that were expressed ubiquitously or in similar groups of tissues such as digestive organs and muscle. Clustering of expression profiles was observed in embryonic brain, postnatal cerebellum, and adult olfactory bulb, reflecting similarities in neurogenesis and remodeling. Finally, clustering genes coding for known enzymes into 78 metabolic pathways revealed a surprising coordination of expression within each pathway among different tissues. On the other hand, a more detailed examination of glycolysis revealed tissue-specific differences in profiles of key regulatory enzymes. Thus, by surveying global gene expression by using microarrays with a large number of elements, we provide insights into the commonality and diversity of pathways responsible for the development and maintenance of the mammalian body plan.

Microsatellite variability and genetic distances.

We analyze the within- and between-population dynamics of the distribution of the number of repeats at multiple microsatellite DNA loci subject to stepwise mutation. Analytical expressions for moments up to the fourth order within a locus and the variance of between-locus variance at mutation-drift equilibrium have been obtained. These statistics may be used to test the appropriateness of the one-step mutation model and to detect between-locus variation in the mutation rate. Published data are compatible with the one-step mutation model, although they do not reject the two-step model. Using both multinomial sampling and diffusion approximations for the analysis of the genetic distance introduced by Goldstein et al. [Goldstein, D. B., Linares, A. R., Cavalli-Sforza, L. L. & Feldman, M. W. (1995) Proc. Natl. Acad. Sci. USA 92, 6723-6727], we show that this distance follows a chi 2 distribution with degrees of freedom equal to the number of loci when there is no variation in mutation rates among the loci. In the presence of such variation, the variance of the distance is obtained. We conclude that the number of microsatellite loci required for the construction of phylogenetic trees with reliable branch lengths may be several hundred. Also, mutations that change repeat scores by several units, even though extremely rare, may dramatically influence estimates of population parameters.

CD38 ligation induces tyrosine phosphorylation of Bruton tyrosine kinase and enhanced expression of interleukin 5-receptor alpha chain: synergistic effects with interleukin 5.

Mouse CD38 has been implicated in the regulation of both B-cell proliferation and protection of B cells from irradiation-induced apoptosis. CD38 ligation on B cells by CS/2, an anti-mouse CD38 monoclonal antibody, induced proliferation, IgM secretion, and tyrosine phosphorylation of Bruton tyrosine kinase in B cells from wild-type mice. B cells from X chromosome-linked immunodeficient mice did not respond at all to anti-CD38 antibody, although CD38 expression on these B cells was comparable to that on wild-type B cells. We infer from these results that Bruton tyrosine kinase activation is involved in B-cell triggering after cross-linkage of CD38. Analysis of the synergistic effects of various cytokines with CD38 ligation on B-cell activation revealed that interleukin 5 (IL-5) showed the most potent effect on B-cell proliferation, Blimp1 gene expression, and IgM production. These synergistic effects were not seen with B cells from X chromosome-linked immunodeficient mice. Flow cytometry analysis revealed that CD38 ligation increased surface expression of the IL-5-receptor alpha chain on B cells. These data indicate that CD38 ligation increases IL-5 receptor alpha expression and synergizes with IL-5 to enhance Blimp1 expression and IgM synthesis.

Evidence that the pathway of disulfide bond formation in Escherichia coli involves interactions between the cysteines of DsbB and DsbA.

Disulfide bond formation is catalyzed in the periplasm of Escherichia coli. This process involves at least two proteins: DsbA and DsbB. Recent evidence suggests that DsbA, a soluble periplasmic protein directly catalyzes disulfide bond formation in proteins, whereas DsbB, an inner membrane protein, is involved in the reoxidation of DsbA. Here we present direct evidence of an interaction between DsbA and DsbB. (Kishigami et al. [Kishigami, S., Kanaya, E., Kikuchi, M. & Ito, K. (1995) J. Biol. Chem. 270, 17072-17074] have described similar findings.) We isolated a dominant negative mutant of dsbA, dsbAd, where Cys-33 of the DsbA active site is changed to tyrosine. Both DsbAd and DsbA are able to form a mixed disulfide with DsbB, which may be an intermediate in the reoxidation of DsbA. This complex is more stable with DsbAd. The dominance can be suppressed by increasing the production of DsbB. By using mutants of DsbB in which one or two cysteines have been changed to alanine, we show that only Cys-104 is important for complex formation. Therefore, we suggest that in vivo, reduced DsbA forms a complex with DsbB in which Cys-30 of DsbA is disulfide-bonded to Cys-104 of DsbB. Cys-104 is rapidly replaced by Cys-33 of DsbA to generate the oxidized form of this protein.

D1 cap region involved in the receptor recognition and neural cell survival activity of human ciliary neurotrophic factor.

Human ciliary neurotrophic factor (hCNTF), which promotes the cell survival and differentiation of motor and other neurons, is a protein belonging structurally to the alpha-helical cytokine family. hCNTF was subjected to three-dimensional structure modeling and site-directed mutagenesis to analyze its structure-function relationship. The replacement of Lys-155 with any other amino acid residue resulted in abolishment of neural cell survival activity, and some of the Glu-153 mutant proteins had 5- to 10-fold higher biological activity. The D1 cap region (around the boundary between the CD loop and helix D) of hCNTF, including both Glu-153 and Lys-155, was shown to play a key role in the biological activity of hCNTF as one of the putative receptor-recognition sites. In this article, the D1 cap region of the 4-helix-bundle proteins is proposed to be important in receptor recognition and biological activity common to alpha-helical cytokine proteins reactive with gp130, a component protein of the receptors.

Replication factor encoded by a putative oncogene, set, associated with myeloid leukemogenesis.

DNA replication of the adenovirus genome complexed with viral core proteins is dependent on the host factor designated template activating factor I (TAF-I) in addition to factors required for replication of the naked genome. Recently, we have purified TAF-I as 39- and 41-kDa polypeptides from HeLa cells. Here we describe the cloning of two human cDNAs encoding TAF-I. Nucleotide sequence analysis revealed that the 39-kDa polypeptide corresponds to the protein encoded by the set gene, which is the part of the putative oncogene associated with acute undifferentiated leukemia when translocated to the can gene. The 41-kDa protein contains the same amino acid sequence as the 39-kDa protein except that short N-terminal regions differ in both proteins. Recombinant proteins, which were purified from extracts of Escherichia coli, expressing the proteins from cloned cDNAs, possessed TAF-I activities in the in vitro replication assay. A particular feature of TAF-I proteins is the presence of a long acidic tail in the C-terminal region, which is thought to be an essential part of the SET-CAN fusion protein. Studies with mutant TAF-I proteins devoid of this acidic region indicated that the acidic region is essential for TAF-I activity.

Incorporação do espalhamento Compton no modelo de TBC modificado

No último século, houve grande avanço no entendimento das interações das radiações com a matéria. Essa compreensão se faz necessária para diversas aplicações, entre elas o uso de raios X no diagnóstico por imagens. Neste caso, imagens são formadas pelo contraste resultante da diferença na atenuação dos raios X pelos diferentes tecidos do corpo. Entretanto, algumas das interações dos raios X com a matéria podem levar à redução da qualidade destas imagens, como é o caso dos fenômenos de espalhamento. Muitas abordagens foram propostas para estimar a distribuição espectral de fótons espalhados por uma barreira, ou seja, como no caso de um feixe de campo largo, ao atingir um plano detector, tais como modelos que utilizam métodos de Monte Carlo e modelos que utilizam aproximações analíticas. Supondo-se um espectro de um feixe primário que não interage com nenhum objeto após sua emissão pelo tubo de raios X, este espectro é, essencialmente representado pelos modelos propostos anteriormente. Contudo, considerando-se um feixe largo de radiação X, interagindo com um objeto, a radiação a ser detectada por um espectrômetro, passa a ser composta pelo feixe primário, atenuado pelo material adicionado, e uma fração de radiação espalhada. A soma destas duas contribuições passa a compor o feixe resultante. Esta soma do feixe primário atenuado, com o feixe de radiação espalhada, é o que se mede em um detector real na condição de feixe largo. O modelo proposto neste trabalho visa calcular o espectro de um tubo de raios X, em situação de feixe largo, o mais fidedigno possível ao que se medem em condições reais. Neste trabalho se propõe a discretização do volume de interação em pequenos elementos de volume, nos quais se calcula o espalhamento Compton, fazendo uso de um espectro de fótons gerado pelo Modelo de TBC, a equação de Klein-Nishina e considerações geométricas. Por fim, o espectro de fótons espalhados em cada elemento de volume é somado ao espalhamento dos demais elementos de volume, resultando no espectro total espalhado. O modelo proposto foi implementado em ambiente computacional MATLAB® e comparado com medições experimentais para sua validação. O modelo proposto foi capaz de produzir espectros espalhados em diferentes condições, apresentando boa conformidade com os valores medidos, tanto em termos quantitativos, nas quais a diferença entre kerma no ar calculado e kerma no ar medido é menor que 10%, quanto qualitativos, com fatores de mérito superiores a 90%.

Reforma del estado como mecanismo de control en democracia delegativa: caso reforma judicial Ecuador 2007-2014

The object of this doctoral thesis is the analysis of the political and administrative purpose that is given to the reform process of a vital sector of State powers within the framework of delegate democracy, such as the administration of Justice. The object is also to analyze if State reform in a diminished or non-liberal surrounding increase or improve conditions of democracy in a given situation, based on the constitutional “what should be”, or if what occurs is a process of “seizure” of the functions of State, which becomes an institutional risk. Finally, we will examine the real and effective existence of a horizontal accountability process through the use of institutional resources, which would evidence the existence of an incomplete model of democracy. This analysis implies the relationship between two institutions within public administration: State Reform, as an act of change in State structure in order to improve qualitatively the outcomes and outputs of public policies, and in sum, to make the system work better. This, as it will be examined later, is the case of Latin America as a response of the State to three processes in crisis: fiscal, as in government intervention or in the form of bureaucratic administration. In that scheme of things, this thesis examines the present state of the art in public administration science of this process to prove that in delegate democracy, this type of instruments disregard the constitutive elements of democracy and serve, especially in critical areas of the administration, allowing for Power to dismiss Law. This research seeks to contribute towards an area seldom analyzed regarding public administration doctrine under the light of the theory of law, which is the connection between previous conditions or principal inputs of an execution process of a democracy and, on the other hand, regarding the effects of introducing a reform within models of a changing democracy and new concepts of the rule of law. While reviewing writings regarding State reform, it is clear that no approximations have been previously made in reference to prior conditions of the political system in order to begin operating a reform which respects fundamental rights as an object of this procedure. Furthermore, no analysis has been found regarding structural change of strategic areas in State services as to the effect caused on democratic exercise and the outcome in an open society...

Hybrid convex combinations for IIR system identification.

The low complexity of IIR adaptive filters (AFs) is specially appealing to realtime applications but some drawbacks have been preventing their widespread use so far. For gradient based IIR AFs, adverse operational conditions cause convergence problems in system identification scenarios: underdamped and clustered poles, undermodelling or non-white input signals lead to error surfaces where the adaptation nearly stops on large plateaus or get stuck at sub-optimal local minima that can not be identified as such a priori. Furthermore, the non-stationarity in the input regressor brought by the filter recursivity and the approximations made by the update rules of the stochastic gradient algorithms constrain the learning step size to small values, causing slow convergence. In this work, we propose IIR performance enhancement strategies based on hybrid combinations of AFs that achieve higher convergence rates than ordinary IIR AFs while keeping the stability.

Coordination of aproximations in secondary school students’ understanding of limit concept

The aim of this research is to characterize the coordination of the processes of approximation related to the understanding of the limit of a function. We analyze the answers of 64 post-secondary school students to 7 problems considering the dynamic and metric conception of limit of a function. Results indicate that the metric understanding of the limit in terms of inequality supports that the student is capable of coordinating the approximations in the domain and in the range when lateral approximations coincide. However, the student is not capable of this coordination when lateral approximations do not coincide. This indicates that the metric understanding of the limit begins with the previous construction of the dynamic conception in case of coincidence of the lateral approximations in the range.

La comprensión de la aproximación a un número en el acceso al significado de límite de una función en un punto

Esta investigación estudia la influencia de la comprensión de la aproximación a un número y de los modos de representación en la construcción de la concepción dinámica del límite en estudiantes de Bachillerato. El análisis de realizó usando el análisis implicativo (Gras, Suzuki, Guillet y Spagnolo, 2008). Los resultados indican que la construcción paulatina de la concepción dinámica del límite se realiza mediante procesos diferenciados de aproximación en el dominio y en el rango, y, dentro de estos últimos, aquellos en los que las aproximaciones laterales coinciden de las que no coinciden. Además, nuestros resultados indican que el modo numérico o el modo algebraico-numérico desempeñan un papel relevante en el desarrollo de la comprensión de la concepción dinámica de límite.

Theory of ferromagnetism in planar heterostructures of (Mn,III)-V semiconductors

A density-functional theory of ferromagnetism in heterostructures of compound semiconductors doped with magnetic impurities is presented. The variable functions in the density-functional theory are the charge and spin densities of the itinerant carriers and the charge and localized spins of the impurities. The theory is applied to study the Curie temperature of planar heterostructures of III-V semiconductors doped with manganese atoms. The mean-field, virtual-crystal and effective-mass approximations are adopted to calculate the electronic structure, including the spin-orbit interaction, and the magnetic susceptibilities, leading to the Curie temperature. By means of these results, we attempt to understand the observed dependence of the Curie temperature of planar δ-doped ferromagnetic structures on variation of their properties. We predict a large increase of the Curie temperature by additional confinement of the holes in a δ-doped layer of Mn by a quantum well.

Spin separation in digital ferromagnetic heterostructures

In a study of the ferromagnetic phase of a multilayer digital ferromagnetic semiconductor in the mean-field and effective-mass approximations, we find the exchange interaction to have the dominant energy scale of the problem, effectively controlling the spatial distribution of the carrier spins in the digital ferromagnetic heterostructures. In the ferromagnetic phase, the majority-spin and minority-spin carriers tend to be in different regions of the space (spin separation). Hence, the charge distribution of carriers also changes noticeably from the ferromagnetic to the paramagnetic phase. An example of a design to exploit these phenomena is given here.

Prediction of hidden multiferroic order in graphene zigzag ribbons

An electronic phase with coexisting magnetic and ferroelectric order is predicted for graphene ribbons with zigzag edges. The electronic structure of the system is described with a mean-field Hubbard model that yields results very similar to those of density functional calculations. Without further approximations, the mean-field theory is recasted in terms of a BCS wave function for electron-hole pairs in the edge bands. The BCS coherence present in each spin channel is related to spin-resolved electric polarization. Although the total electric polarization vanishes, due to an internal phase locking of the BCS state, strong magnetoelectric effects are expected in this system. The formulation naturally accounts for the two gaps in the quasiparticle spectrun, Δ0 and Δ1, and relates them to the intraband and interband self-energies.

Tunnel magnetoresistance in GaMnAs: going beyond Jullière formula

The relation between tunnel magnetoresistance (TMR) and spin polarization is explored for GaMnAs∕GaAlAs∕GaMnAs structures where the carriers experience strong spin–orbit interactions. TMR is calculated using the Landauer approach. The materials are described in the 6 band k⋅p model which includes spin–orbit interaction. Ferromagnetism is described in the virtual crystal mean field approximations. Our results indicate that TMR is a function of spin polarization and barrier thickness. As a result of the stong spin–orbit interactions, TMR also depends on the the angle between current flow direction and the electrode magnetization. These results compromise the validity of Julliere formula.