A T42A Ran Mutation: Differential Interactions with Effectors and Regulators, and Defect in Nuclear Protein Import

Ran, the small, predominantly nuclear GTPase, has been implicated in the regulation of a variety of cellular processes including cell cycle progression, nuclear-cytoplasmic trafficking of RNA and protein, nuclear structure, and DNA synthesis. It is not known whether Ran functions directly in each process or whether many of its roles may be secondary to a direct role in only one, for example, nuclear protein import. To identify biochemical links between Ran and its functional target(s), we have generated and examined the properties of a putative Ran effector mutation, T42A-Ran. T42A-Ran binds guanine nucleotides as well as wild-type Ran and responds as well as wild-type Ran to GTP or GDP exchange stimulated by the Ran-specific guanine nucleotide exchange factor, RCC1. T42A-Ran·GDP also retains the ability to bind p10/NTF2, a component of the nuclear import pathway. In contrast to wild-type Ran, T42A-Ran·GTP binds very weakly or not detectably to three proposed Ran effectors, Ran-binding protein 1 (RanBP1), Ran-binding protein 2 (RanBP2, a nucleoporin), and karyopherin ß (a component of the nuclear protein import pathway), and is not stimulated to hydrolyze bound GTP by Ran GTPase-activating protein, RanGAP1. Also in contrast to wild-type Ran, T42A-Ran does not stimulate nuclear protein import in a digitonin permeabilized cell assay and also inhibits wild-type Ran function in this system. However, the T42A mutation does not block the docking of karyophilic substrates at the nuclear pore. These properties of T42A-Ran are consistent with its classification as an effector mutant and define the exposed region of Ran containing the mutation as a probable effector loop.

Hepatocyte nuclear factor-4 alpha regulates the human apolipoprotein AV gene: Identification of a novel response element and involvement in the control by peroxisome proliferator-activated receptor-gamma coactivator-1 alpha, AMP-activated protein kinase, and mitogen-activated protein kinase pathway

The recently discovered apolipoprotein AV (apoAV) gene has been reported to be a key player in modulating plasma triglyceride levels. Here we identify the hepatocyte nuclear factor-4 (HNF-4 ) as a novel regulator of human apoAV gene. Inhibition of HNF-4 expression by small interfering RNA resulted in down-regulation of apoAV. Deletion, mutagenesis, and binding assays revealed that HNF-4 directly regulates human apoAV promoter through DR1 [a direct repeat separated by one nucleotide (nt)], and via a novel element for HNF-4 consisting of an inverted repeat separated by 8 nt (IR8). In addition, we show that the coactivator peroxisome proliferator-activated receptor- coactivator-1 was capable of stimulating the HNF-4 -dependent transactivation of apoAV promoter. Furthermore, analyses in human hepatic cells demonstrated that AMP-activated protein kinase (AMPK) and the MAPK signaling pathway regulate human apoAV expression and suggested that this regulation may be mediated, at least in part, by changes in HNF-4 . Intriguingly, EMSAs and mice with a liver-specific disruption of the HNF-4 gene revealed a species-distinct regulation of apoAV by HNF-4 , which resembles that of a subset of HNF-4 target genes. Taken together, our data provide new insights into the binding properties and the modulation of HNF-4 and underscore the role of HNF-4 in regulating triglyceride metabolism.

Classical cross sections for relativistic spinning particles

We propose a definition of classical differential cross sections for particles with essentially nonplanar orbits, such as spinning ones. We give also a method for its computation. The calculations are carried out explicitly for electromagnetic, gravitational, and short-range scalar interactions up to the linear terms in the slow-motion approximation. The contribution of the spin-spin terms is found to be at best 10-6 times the post-Newtonian ones for the gravitational interaction.

Polychlorinated trityl radicals for dynamic nuclear polarization: the role of chlorine nuclei

Polychlorinated trityl radicals bearing carboxylate substituents are water soluble persistent radicals that can be used for dynamic nuclear polarization. In contrast to other trityl radicals, the polarization mechanism differs from the classical solid effect. DFT calculations performed to rationalize this behaviour support the hypothesis that polarization is transferred from the unpaired electron to chlorine nuclei and from these to carbon by spin diffusion. The marked differences observed between neutral and anionic forms of the radical will be discussed.

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

BACKGROUND: The p53 transcription factor is located at the core of a complex wiring of signaling pathways that are critical for the preservation of cellular homeostasis. Only recently it has become clear that p53 regulates the expression of several long intergenic noncoding RNAs (lincRNAs). However, relatively little is known about the role that lincRNAs play in this pathway. RESULTS: Here we characterize a lincRNA named Pint (p53 induced noncoding transcript). We show that Pint is a ubiquitously expressed lincRNA that is finely regulated by p53. In mouse cells, Pint promotes cell proliferation and survival by regulating the expression of genes of the TGF-β, MAPK and p53 pathways. Pint is a nuclear lincRNA that directly interacts with the Polycomb repressive complex 2 (PRC2), and is required for PRC2 targeting of specific genes for H3K27 tri-methylation and repression. Furthermore, Pint functional activity is highly dependent on PRC2 expression. We have also identified Pint human ortholog (PINT), which presents suggestive analogies with the murine lincRNA. PINT is similarly regulated by p53, and its expression significantly correlates with the same cellular pathways as the mouse ortholog, including the p53 pathway. Interestingly, PINT is downregulated in colon primary tumors, while its overexpression inhibits the proliferation of tumor cells, suggesting a possible role as tumor suppressor. CONCLUSIONS: Our results reveal a p53 autoregulatory negative mechanism where a lincRNA connects p53 activation with epigenetic silencing by PRC2. Additionally, we show analogies and differences between the murine and human orthologs, identifying a novel tumor suppressor candidate lincRNA.

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae

Background: Current advances in genomics, proteomics and other areas of molecular biology make the identification and reconstruction of novel pathways an emerging area of great interest. One such class of pathways is involved in the biogenesis of Iron-Sulfur Clusters (ISC). Results: Our goal is the development of a new approach based on the use and combination of mathematical, theoretical and computational methods to identify the topology of a target network. In this approach, mathematical models play a central role for the evaluation of the alternative network structures that arise from literature data-mining, phylogenetic profiling, structural methods, and human curation. As a test case, we reconstruct the topology of the reaction and regulatory network for the mitochondrial ISC biogenesis pathway in S. cerevisiae. Predictions regarding how proteins act in ISC biogenesis are validated by comparison with published experimental results. For example, the predicted role of Arh1 and Yah1 and some of the interactions we predict for Grx5 both matches experimental evidence. A putative role for frataxin in directly regulating mitochondrial iron import is discarded from our analysis, which agrees with also published experimental results. Additionally, we propose a number of experiments for testing other predictions and further improve the identification of the network structure. Conclusion: We propose and apply an iterative in silico procedure for predictive reconstruction of the network topology of metabolic pathways. The procedure combines structural bioinformatics tools and mathematical modeling techniques that allow the reconstruction of biochemical networks. Using the Iron Sulfur cluster biogenesis in S. cerevisiae as a test case we indicate how this procedure can be used to analyze and validate the network model against experimental results. Critical evaluation of the obtained results through this procedure allows devising new wet lab experiments to confirm its predictions or provide alternative explanations for further improving the models.

Saccharomyces cerevisiae Grx6 and Grx7 are monothiol glutaredoxins associated with the early secretory pathway

Saccharomyces cerevisiae Grx6 and Grx7 are two monothiol glutaredoxins whose active-site sequences (CSYS and CPYS, respectively) are reminiscent of the CPYC active-site sequence of classical dithiol glutaredoxins. Both proteins contain an N-terminal transmembrane domain which is responsible for their association to membranes of the early secretory pathway vesicles, facing the luminal side. Thus, Grx6 localizes at the endoplasmic reticulum and Golgi compartments, while Grx7 is mostly at the Golgi. Expression of GRX6 is modestly upregulated by several stresses (calcium, sodium, and peroxides) in a manner dependent on the Crz1-calcineurin pathway. Some of these stresses also upregulate GRX7 expression under the control of the Msn2/4 transcription factor. The N glycosylation inhibitor tunicamycin induces the expression of both genes along with protein accumulation. Mutants lacking both glutaredoxins display reduced sensitivity to tunicamycin, although the drug is still able to manifest its inhibitory effect on a reporter glycoprotein. Grx6 and Grx7 have measurable oxidoreductase activity in vivo, which is increased in the presence of tunicamycin. Both glutaredoxins could be responsible for the regulation of the sulfhydryl oxidative state at the oxidant conditions of the early secretory pathway vesicles. However, the differences in location and expression responses against stresses suggest that their functions are not totally overlapping.

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

BACKGROUND: The p53 transcription factor is located at the core of a complex wiring of signaling pathways that are critical for the preservation of cellular homeostasis. Only recently it has become clear that p53 regulates the expression of several long intergenic noncoding RNAs (lincRNAs). However, relatively little is known about the role that lincRNAs play in this pathway. RESULTS: Here we characterize a lincRNA named Pint (p53 induced noncoding transcript). We show that Pint is a ubiquitously expressed lincRNA that is finely regulated by p53. In mouse cells, Pint promotes cell proliferation and survival by regulating the expression of genes of the TGF-β, MAPK and p53 pathways. Pint is a nuclear lincRNA that directly interacts with the Polycomb repressive complex 2 (PRC2), and is required for PRC2 targeting of specific genes for H3K27 tri-methylation and repression. Furthermore, Pint functional activity is highly dependent on PRC2 expression. We have also identified Pint human ortholog (PINT), which presents suggestive analogies with the murine lincRNA. PINT is similarly regulated by p53, and its expression significantly correlates with the same cellular pathways as the mouse ortholog, including the p53 pathway. Interestingly, PINT is downregulated in colon primary tumors, while its overexpression inhibits the proliferation of tumor cells, suggesting a possible role as tumor suppressor. CONCLUSIONS: Our results reveal a p53 autoregulatory negative mechanism where a lincRNA connects p53 activation with epigenetic silencing by PRC2. Additionally, we show analogies and differences between the murine and human orthologs, identifying a novel tumor suppressor candidate lincRNA.

Genetic Variation in the TP53 Pathway and Bladder Cancer Risk. A Comprehensive Analysis

Introduction: Germline variants in TP63 have been consistently associated with several tumors, including bladder cancer, indicating the importance of TP53 pathway in cancer genetic susceptibility. However, variants in other related genes, including TP53 rs1042522 (Arg72Pro), still present controversial results. We carried out an in depth assessment of associations between common germline variants in the TP53 pathway and bladder cancer risk. Material and Methods: We investigated 184 tagSNPs from 18 genes in 1,058 cases and 1,138 controls from the Spanish Bladder Cancer/EPICURO Study. Cases were newly-diagnosed bladder cancer patients during 1998–2001. Hospital controls were age-gender, and area matched to cases. SNPs were genotyped in blood DNA using Illumina Golden Gate and TaqMan assays. Cases were subphenotyped according to stage/grade and tumor p53 expression. We applied classical tests to assess individual SNP associations and the Least Absolute Shrinkage and Selection Operator (LASSO)-penalized logistic regression analysis to assess multiple SNPs simultaneously. Results: Based on classical analyses, SNPs in BAK1 (1), IGF1R (5), P53AIP1 (1), PMAIP1 (2), SERINPB5 (3), TP63 (3), and TP73 (1) showed significant associations at p-value#0.05. However, no evidence of association, either with overall risk or with specific disease subtypes, was observed after correction for multiple testing (p-value$0.8). LASSO selected the SNP rs6567355 in SERPINB5 with 83% of reproducibility. This SNP provided an OR = 1.21, 95%CI 1.05–1.38, p-value = 0.006, and a corrected p-value = 0.5 when controlling for over-estimation. Discussion: We found no strong evidence that common variants in the TP53 pathway are associated with bladder cancer susceptibility. Our study suggests that it is unlikely that TP53 Arg72Pro is implicated in the UCB in white Europeans. SERPINB5 and TP63 variation deserve further exploration in extended studies.

Digitalización del sistema de control de nivel en calentadores y tanques de drenaje de una Central Nuclear

Contexto Una central nuclear, al igual que cualquier otro tipo de central generadora de energía eléctrica, mediante turbinas de vapor, está basada en un proceso termodinámico. El rendimiento de las mismas es función del salto entálpico del vapor, para mejorarlo las centrales están constituidas por un ciclo compound formado por turbina de alta presión y turbinas de baja presión, y un ciclo regenerativo consistente en calentar el agua de alimentación antes de su introducción a los generadores de vapor. Un ciclo regenerativo está basado en etapas de calentadores o cambiadores de calor para aprovechar al máximo la energía térmica del vapor, este proyecto está basado en la mejora y optimización del proceso de control de estos para contribuir a mejorar el rendimiento de la central. Objetivo Implementar un sistema de control que nos permita modernizar los clásicos sistemas basados en controles locales y comunicaciones analógicas. Mejorar el rendimiento del ciclo regenerativo de la central, aprovechando las mejoras tecnológicas que ofrece el mercado, tanto en el hardware como en el software de los sistemas de instrumentación y control. Optimizar el rendimiento de los lazos de control de cada uno de los elementos del ciclo regenerativo mediante estrategias de control. Procedimiento Desarrollo de un sistema de control actualizado considerando, como premisa principal, la fiabilidad del sistema, el análisis de fallos y la jerarquización del riesgo. Análisis y cálculo de los lazos de control considerando las premisas establecidas. Configuración de los lazos mediante estrategias de control que nos permitan optimizar y minimizar los efectos del fallo. Para ello se han utilizado parámetros y datos extraídos de la Central Nuclear de Ascó. Conclusiones Se ha modernizado y optimizado el sistema de control mejorando el rendimiento del ciclo regenerativo. Se ha conseguido un sistema más fiable, reduciendo el riesgo del fallo y disminuyendo los efectos de los mismos. El coste de un proyecto de estas características es inferior al de un sistema convencional y ofrece más posibilidades. Es un sistema abierto que permite utilizar e interconectar equipos de diferentes fabricantes, lo que favorece tanto el mantenimiento como las posibles ampliaciones futuras del sistema.

Classical line shapes based on analytical solutions of bimolecular trajectories in collision induced emission. II. Reactive collisions

The classical theory of collision induced emission (CIE) from pairs of dissimilar rare gas atoms was developed in Paper I [D. Reguera and G. Birnbaum, J. Chem. Phys. 125, 184304 (2006)] from a knowledge of the straight line collision trajectory and the assumption that the magnitude of the dipole could be represented by an exponential function of the inter-nuclear distance. This theory is extended here to deal with other functional forms of the induced dipole as revealed by ab initio calculations. Accurate analytical expression for the CIE can be obtained by least square fitting of the ab initio values of the dipole as a function of inter-atomic separation using a sum of exponentials and then proceeding as in Paper I. However, we also show how the multi-exponential fit can be replaced by a simpler fit using only two analytic functions. Our analysis is applied to the polar molecules HF and HBr. Unlike the rare gas atoms considered previously, these atomic pairs form stable bound diatomic molecules. We show that, interestingly, the spectra of these reactive molecules are characterized by the presence of multiple peaks. We also discuss the CIE arising from half collisions in excited electronic states, which in principle could be probed in photo-dissociation experiments.

Classical horizontal inequity and reranking: an integrated approach

The last 20 years have seen a significant evolution in the literature on horizontal inequity (HI) and have generated two major and "rival" methodological strands, namely, classical HI and reranking. We propose in this paper a class of ethically flexible tools that integrate these two strands. This is achieved using a measure of inequality that merges the well-known Gini coefficient and Atkinson indices, and that allows a decomposition of the total redistributive effect of taxes and transfers in a vertical equity effect and a loss of redistribution due to either classical HI or reranking. An inequality-change approach and a money-metric cost-of-inequality approach are developed. The latter approach makes aggregate classical HI decomposable across groups. As in recent work, equals are identified through a nonparametric estimation of the joint density of gross and net incomes. An illustration using Canadian data from 1981 to 1994 shows a substantial, and increasing, robust erosion of redistribution attributable both to classical HI and to reranking, but does not reveal which of reranking or classical HI is more important since this requires a judgement that is fundamentally normative in nature.

Nuclear Weapons as Symbols. The Role of Norms in Nuclear Policy Making

Throughout history, nuclear weapons have been considered to be the ultimate weapons. This understanding largely detached them from the portfolio of conventional military means and assigned them a symbolic meaning that influenced the identity and norms creation of nations. In most countries today, the development of nuclear weapons is considered morally prohibitive, incompatible with a country’s identity and international outlook. In some states, however, these negative norms are overridden by a positive set of norms, causing nuclear weapons to become either symbols of invulnerability to perceived threats or the regalia of major power status. Main purpose of this paper is to explore on the conditions that cause most states to develop a moral aversion to nuclear weapons, yet effectively lead to their glorification in others. Many studies on the normative understanding of nuclear weapons consider the existence of a negative normative predisposition, often referred to as ‘nuclear taboo’, as a major factor in preventing their acquisition and use. Other studies acknowledge the existence of a nuclear taboo inhibiting the use of nuclear weapons, but point to the existence of the opposing effect of norms, frequently referred to as the ‘nuclear myth’, when it comes to the acquisition of nuclear weapons. This myth emerges when certain symbolic meanings are attached to nuclear weapons, such as a state’s identity, self-image, and its desired position in the international system. With 180 odd countries in the world abstaining from the acquisition of nuclear weapons and 8 countries in possession of them (with two further countries assumed to have pursued their acquisition), one might consider the dominance of the nuclear taboo over the nuclear myth to be the rule. The core question is thus why and how this relationship reversed in the case of defectors.

Caracterización agronómica, fenológica, cualitativa y molecular de la colección nuclear de cebadas españolas

El presente proyecto planteaba el paso siguiente a la construcción, por nosotros mismos, de la Colección Nuclear de Cebadas Españolas, que es una representación esquemática de la variabilidad genética de las cebadas ancestralmente cultivadas en nuestro país. Para la explotación completa de estos materiales autóctonos en el Programa Nacional de Mejora de Cebadas, que estamos llevando a cabo los grupos integrantes de este proyecto, se realizó el mismo, que ha comprendido los objetivos siguientes: - Caracterización agronómica, mediante ensayos de campo en ambientes contrastantes y representativos, incluyendo la evaluación de respuestas a factores productores de estreses bióticos y abióticos. - Caracterización fenológica, mediante ensayos en invernadero con protocolos desarrollados por nosotros, para identificar la respuesta de estos genotipos a la vernalización y el fotoperiodo. - Caracterización maltero-cervecera/pienso, mediante análisis de cebada y malta. - Caracterización molecular, mediante el uso de marcadores SSRs y STS.