Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

Relation for the nonequilibrium population of the interface states: effects on the bias dependence of the ideality factors

By an analysis of the exchange of carriers through a semiconductor junction, a general relationship for the nonequilibrium population of the interface states in Schottky barrier diodes has been derived. Based on this relationship, an analytical expression for the ideality factor valid in the whole range of applied bias has been given. This quantity exhibits two different behaviours depending on the value of the applied bias with respect to a critical voltage. This voltage, which depends on the properties of the interfacial layer, constitutes a new parameter to complete the characterization of these junctions. A simple interpretation of the different behaviours of the ideality factor has been given in terms of the nonequilibrium charging properties of interface states, which in turn explains why apparently different approaches have given rise to similar results. Finally, the relevance of our results has been considered on the determination of the density of interface states from nonideal current-voltage characteristics and in the evaluation of the effects of the interfacial layer thickness in metal-insulator-semiconductor tunnelling diodes.

Electric-field control of exchange bias in multiferroic epitaxial heterostructures

The magnetic exchange between epitaxial thin films of the multiferroic (antiferromagnetic and ferroelectric) hexagonal YMnO3 oxide and a soft ferromagnetic (FM) layer is used to couple the magnetic response of the FM layer to the magnetic state of the antiferromagnetic one. We will show that biasing the ferroelectric YMnO3 layer by an electric field allows control of the magnetic exchange bias and subsequently the magnetotransport properties of the FM layer. This finding may contribute to paving the way towards a new generation of electric-field controlled spintronic devices.

Exchange bias between magnetoelectric YMnO3 and ferromagnetic SrRuO3 epitaxial films

Orthorhombic YMnO3 (YMO) epitaxial thin films were deposited on SrTiO3 (STO) single-crystal substrates. We show that the out-of-plane texture of the YMO films can be tailored using STO substrates having (001), (110), or (111) orientations. We report on the magnetic properties of the YMO(010) films grown on STO(001) substrates. The dependence of the susceptibility on the temperature indicates that the films are antiferromagnetic below the Néel temperature (around 35 K). Orthorhombic YMO(010) films were also deposited on an epitaxial buffer layer of ferromagnetic and metallic SrRuO3 (SRO). The magnetic hysteresis loops of SRO show exchange bias at temperatures below the Néel temperature of YMO. These results confirm that the YMO films are antiferromagnetic and demonstrate that magnetoelectric YMO can be integrated in functional epitaxial architectures.

Microscopic origin of exchange bias in core/shell nanoparticles

We report the results of Monte Carlo simulations with the aim to clarify the microscopic origin of exchange bias in the magnetization hysteresis loops of a model of individual core/shell nanoparticles. Increase of the exchange coupling across the core/shell interface leads to an enhancement of exchange bias and to an increasing asymmetry between the two branches of the loops which is due to different reversal mechanisms. A detailed study of the magnetic order of the interfacial spins shows compelling evidence that the existence of a net magnetization due to uncompensated spins at the shell interface is responsible for both phenomena and allows to quantify the loop shifts directly in terms of microscopic parameters with striking agreement with the macroscopic observed values.

Depth profile of uncompensated spins in an exchange bias system

We have used the unique spatial sensitivity of polarized neutron and soft x-ray beams in reflection geometry to measure the depth dependence of magnetization across the interface between a ferromagnet and an antiferromagnet. The net uncompensated magnetization near the interface responds to applied field, while uncompensated spins in the antiferromagnet bulk are pinned, thus providing a means to establish exchange bias.

Relation for the nonequilibrium population of the interface states: effects on the bias dependence of the ideality factors

By an analysis of the exchange of carriers through a semiconductor junction, a general relationship for the nonequilibrium population of the interface states in Schottky barrier diodes has been derived. Based on this relationship, an analytical expression for the ideality factor valid in the whole range of applied bias has been given. This quantity exhibits two different behaviours depending on the value of the applied bias with respect to a critical voltage. This voltage, which depends on the properties of the interfacial layer, constitutes a new parameter to complete the characterization of these junctions. A simple interpretation of the different behaviours of the ideality factor has been given in terms of the nonequilibrium charging properties of interface states, which in turn explains why apparently different approaches have given rise to similar results. Finally, the relevance of our results has been considered on the determination of the density of interface states from nonideal current-voltage characteristics and in the evaluation of the effects of the interfacial layer thickness in metal-insulator-semiconductor tunnelling diodes.

Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

Background: The arrangement of regulatory motifs in gene promoters, or promoterarchitecture, is the result of mutation and selection processes that have operated over manymillions of years. In mammals, tissue-specific transcriptional regulation is related to the presence ofspecific protein-interacting DNA motifs in gene promoters. However, little is known about therelative location and spacing of these motifs. To fill this gap, we have performed a systematic searchfor motifs that show significant bias at specific promoter locations in a large collection ofhousekeeping and tissue-specific genes.Results: We observe that promoters driving housekeeping gene expression are enriched inparticular motifs with strong positional bias, such as YY1, which are of little relevance in promotersdriving tissue-specific expression. We also identify a large number of motifs that show positionalbias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specificmotifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis,as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictionsfor 559 tissue-specific motifs in mouse gene promoters.Conclusion: The study shows that motif positional bias is an important feature of mammalianproximal promoters and that it affects both general and tissue-specific motifs. Motif positionalconstraints define very distinct promoter architectures depending on breadth of expression andtype of tissue.

Risk aversion and embedding bias

In Selten (1967) ?Strategy Method,? the second mover in the game submits a complete strategy. This basic idea has been exported to nonstrategic experiments, where a participant reports a complete list of contingent decisions, one for each situation or state in a given sequence, out of which one and only one state, randomly selected, will be implemented.In general, the method raises the following concern. If S0 and S1 are two differentsequences of states, and state s is in both S0 and S1, would the participant make the same decision in state s when confronted with S0 as when confronted with S1? If not, the experimental results are suspect of suffering from an ?embedding bias.?We check for embedding biases in elicitation methods of Charles Holt and Susan Laury(Laury and Holt, 2000, and Holt and Laury, 2002), and of the present authors (Bosch-Dom?nech and Silvestre, 1999, 2002, 2006a, b) by appropriately chosen replications of the original experiments. We find no evidence of embedding bias in our work. But in Holt and Laury?s method participants tend to switch earlier to the riskier option when later pairs of lotteries are eliminated from the sequence, suggesting the presence of some embedding bias.

Welfare spending and ethnic heterogeneity. Evidence from a massive immigration wave

[spa] En este trabajo se analiza la relación entre la heterogeneidad étnica y la redistribución, utilizando la reciente y masiva llegada de inmigrantes a España. En concreto, se estudia el efecto de los cambios en la densidad de inmigrantes, observada entre 1998 y 2006, sobre los cambios en el gasto social municipal. La densidad de inmigrantes se instrumenta utilizando los patrones de establecimiento por país de origen para asignar los flujos predichos de inmigrantes a cada municipio. Los resultados evidencian que el gasto social incrementó menos en los municipios con mayores incrementos en la densidad de inmigrantes. También se proporciona evidencia de la existencia de una relación positiva entre la densidad de inmigrantes y el porcentaje de voto obtenidos por los partidos de derecha. Por tanto, estos resultados son consistentes con las teorías que predicen una relación negativa entre la heterogeneidad étnica y la redistribución.

Welfare spending and ethnic heterogeneity. Evidence from a massive immigration wave

[spa] En este trabajo se analiza la relación entre la heterogeneidad étnica y la redistribución, utilizando la reciente y masiva llegada de inmigrantes a España. En concreto, se estudia el efecto de los cambios en la densidad de inmigrantes, observada entre 1998 y 2006, sobre los cambios en el gasto social municipal. La densidad de inmigrantes se instrumenta utilizando los patrones de establecimiento por país de origen para asignar los flujos predichos de inmigrantes a cada municipio. Los resultados evidencian que el gasto social incrementó menos en los municipios con mayores incrementos en la densidad de inmigrantes. También se proporciona evidencia de la existencia de una relación positiva entre la densidad de inmigrantes y el porcentaje de voto obtenidos por los partidos de derecha. Por tanto, estos resultados son consistentes con las teorías que predicen una relación negativa entre la heterogeneidad étnica y la redistribución.

Ethnic identity construction in Chiapas: examining the role of higher intercultural education model = La construcción de la identidad étnica en Chiapas : examinando el rol de un modelo de educación superior intercultural

This study explored ethnic identity among 410 mestizo students who were attending one of three universities, which varied in their ethnic composition and their educative model. One of these universities was private and had mostly mestizo students such as the public one did. The third educative context, also public, had an intercultural model of education and the students were mixed among mestizo and indigenous. The Multigroup Ethnic Identity Measure (MEIM) was administered to high school students in order to compare their scores on ethnic identity and its components: affi rmation, belonging or commitment and exploration. Principle components factor analysis with varimax rotation and tests of mean group differences are performed. The results showed signifi cant differences between the studied groups. Scores on ethnic identity and its components were signifi cantly higher among mestizos group from University with intercultural model of education than mestizos from public and private universities of the same region. Implications of these fi ndings for education are considered, as they are the strengths as well as the limitations of this research

Ethnic Identity among Indigenous and Mestizos from Intercultural University of Chiapas = Identidad étnica entre los indígenas y los mestizos de la Universidad Intercultural de Chiapas

This study explored ethnic identity among 662 students (326 mestizos and 336 indigenous) from the Intercultural University of Chiapas (IUCh). Scholars suggest that ethnicity is more salient for ethnic minority adolescents than for adolescents who are members of the ethnic majority. The aims for this study were: 1) to determine the structure and validity of ethnic identity as measured by the Multigroup Ethnic Identity Measure in a sample of majority and minority ethnic groups from Intercultural University in Chiapas, and 2) to examine the variability of ethnic identity across ethnic groups. Specifically, it was hypothesized that the Multigroup Ethnic Identity Measure would show two factors, and that ethnic groups would differ on ethnic identity. The results supported the hypotheses