Identification and analysis of a nickel-inducible cation diffusion facilitator-NiCoT combined system in Rhizobium leguminosarum bv. viciae

Nickel, like other transition metals, can be toxic to cells even at moderate concentration (low microM range) by displacing essential metals from their native binding sites or by generating reactive oxygen species that cause oxidative DNA damage. For this reason, cells have evolved mechanisms to deal with excess nickel. Efflux systems include members of the Resistance-Nodulation-cell Division (RND) protein family, P-type ATPases, cation diffusion facilitators (CDF) and other resistance factors. Nickel-specific exporters have been characterized in Cupravidus metallidurans, Helicobacter pylori, Achromobacter xylosoxidans, Serratia marcenses and Escherichia coli.

High power beam dump project for the accelerator prototype LIPAc: Cooling design and analysis

En el campo de la fusión nuclear y desarrollándose en paralelo a ITER (International Thermonuclear Experimental Reactor), el proyecto IFMIF (International Fusion Material Irradiation Facility) se enmarca dentro de las actividades complementarias encaminadas a solucionar las barreras tecnológicas que aún plantea la fusión. En concreto IFMIF es una instalación de irradiación cuya misión es caracterizar materiales resistentes a condiciones extremas como las esperadas en los futuros reactores de fusión como DEMO (DEMOnstration power plant). Consiste de dos aceleradores de deuterones que proporcionan un haz de 125 mA y 40 MeV cada uno, que al colisionar con un blanco de litio producen un flujo neutrónico intenso (1017 neutrones/s) con un espectro similar al de los neutrones de fusión [1], [2]. Dicho flujo neutrónico es empleado para irradiar los diferentes materiales candidatos a ser empleados en reactores de fusión, y las muestras son posteriormente examinadas en la llamada instalación de post-irradiación. Como primer paso en tan ambicioso proyecto, una fase de validación y diseño llamada IFMIFEVEDA (Engineering Validation and Engineering Design Activities) se encuentra actualmente en desarrollo. Una de las actividades contempladas en esta fase es la construcción y operación de una acelarador prototipo llamado LIPAc (Linear IFMIF Prototype Accelerator). Se trata de un acelerador de deuterones de alta intensidad idéntico a la parte de baja energía de los aceleradores de IFMIF. Los componentes del LIPAc, que será instalado en Japón, son suministrados por diferentes países europeos. El acelerador proporcionará un haz continuo de deuterones de 9 MeV con una potencia de 1.125 MW que tras ser caracterizado con diversos instrumentos deberá pararse de forma segura. Para ello se requiere un sistema denominado bloque de parada (Beam Dump en inglés) que absorba la energía del haz y la transfiera a un sumidero de calor. España tiene el compromiso de suministrar este componente y CIEMAT (Centro de Investigaciones Energéticas Medioambientales y Tecnológicas) es responsable de dicha tarea. La pieza central del bloque de parada, donde se para el haz de iones, es un cono de cobre con un ángulo de 3.5o, 2.5 m de longitud y 5 mm de espesor. Dicha pieza está refrigerada por agua que fluye en su superficie externa por el canal que se forma entre el cono de cobre y otra pieza concéntrica con éste. Este es el marco en que se desarrolla la presente tesis, cuyo objeto es el diseño del sistema de refrigeración del bloque de parada del LIPAc. El diseño se ha realizado utilizando un modelo simplificado unidimensional. Se han obtenido los parámetros del agua (presión, caudal, pérdida de carga) y la geometría requerida en el canal de refrigeración (anchura, rugosidad) para garantizar la correcta refrigeración del bloque de parada. Se ha comprobado que el diseño permite variaciones del haz respecto a la situación nominal siendo el flujo crítico calorífico al menos 2 veces superior al nominal. Se han realizado asimismo simulaciones fluidodinámicas 3D con ANSYS-CFX en aquellas zonas del canal de refrigeración que lo requieren. El bloque de parada se activará como consecuencia de la interacción del haz de partículas lo que impide cualquier cambio o reparación una vez comenzada la operación del acelerador. Por ello el diseño ha de ser muy robusto y todas las hipótesis utilizadas en la realización de éste deben ser cuidadosamente comprobadas. Gran parte del esfuerzo de la tesis se centra en la estimación del coeficiente de transferencia de calor que es determinante en los resultados obtenidos, y que se emplea además como condición de contorno en los cálculos mecánicos. Para ello por un lado se han buscado correlaciones cuyo rango de aplicabilidad sea adecuado para las condiciones del bloque de parada (canal anular, diferencias de temperatura agua-pared de decenas de grados). En un segundo paso se han comparado los coeficientes de película obtenidos a partir de la correlación seleccionada (Petukhov-Gnielinski) con los que se deducen de simulaciones fluidodinámicas, obteniendo resultados satisfactorios. Por último se ha realizado una validación experimental utilizando un prototipo y un circuito hidráulico que proporciona un flujo de agua con los parámetros requeridos en el bloque de parada. Tras varios intentos y mejoras en el experimento se han obtenido los coeficientes de película para distintos caudales y potencias de calentamiento. Teniendo en cuenta la incertidumbre de las medidas, los valores experimentales concuerdan razonablemente bien (en el rango de 15%) con los deducidos de las correlaciones. Por motivos radiológicos es necesario controlar la calidad del agua de refrigeración y minimizar la corrosión del cobre. Tras un estudio bibliográfico se identificaron los parámetros del agua más adecuados (conductividad, pH y concentración de oxígeno disuelto). Como parte de la tesis se ha realizado asimismo un estudio de la corrosión del circuito de refrigeración del bloque de parada con el doble fin de determinar si puede poner en riesgo la integridad del componente, y de obtener una estimación de la velocidad de corrosión para dimensionar el sistema de purificación del agua. Se ha utilizado el código TRACT (TRansport and ACTivation code) adaptándalo al caso del bloque de parada, para lo cual se trabajó con el responsable (Panos Karditsas) del código en Culham (UKAEA). Los resultados confirman que la corrosión del cobre en las condiciones seleccionadas no supone un problema. La Tesis se encuentra estructurada de la siguiente manera: En el primer capítulo se realiza una introducción de los proyectos IFMIF y LIPAc dentro de los cuales se enmarca esta Tesis. Además se describe el bloque de parada, siendo el diseño del sistema de rerigeración de éste el principal objetivo de la Tesis. En el segundo y tercer capítulo se realiza un resumen de la base teórica así como de las diferentes herramientas empleadas en el diseño del sistema de refrigeración. El capítulo cuarto presenta los resultados del relativos al sistema de refrigeración. Tanto los obtenidos del estudio unidimensional, como los obtenidos de las simulaciones fluidodinámicas 3D mediante el empleo del código ANSYS-CFX. En el quinto capítulo se presentan los resultados referentes al análisis de corrosión del circuito de refrigeración del bloque de parada. El capítulo seis se centra en la descripción del montaje experimental para la obtención de los valores de pérdida de carga y coeficiente de transferencia del calor. Asimismo se presentan los resultados obtenidos en dichos experimentos. Finalmente encontramos un capítulo de apéndices en el que se describen una serie de experimentos llevados a cabo como pasos intermedios en la obtención del resultado experimental del coeficiente de película. También se presenta el código informático empleado para el análisis unidimensional del sistema de refrigeración del bloque de parada llamado CHICA (Cooling and Heating Interaction and Corrosion Analysis). ABSTRACT In the nuclear fusion field running in parallel to ITER (International Thermonuclear Experimental Reactor) as one of the complementary activities headed towards solving the technological barriers, IFMIF (International Fusion Material Irradiation Facility) project aims to provide an irradiation facility to qualify advanced materials resistant to extreme conditions like the ones expected in future fusion reactors like DEMO (DEMOnstration Power Plant). IFMIF consists of two constant wave deuteron accelerators delivering a 125 mA and 40 MeV beam each that will collide on a lithium target producing an intense neutron fluence (1017 neutrons/s) with a similar spectra to that of fusion neutrons [1], [2]. This neutron flux is employed to irradiate the different material candidates to be employed in the future fusion reactors, and the samples examined after irradiation at the so called post-irradiative facilities. As a first step in such an ambitious project, an engineering validation and engineering design activity phase called IFMIF-EVEDA (Engineering Validation and Engineering Design Activities) is presently going on. One of the activities consists on the construction and operation of an accelerator prototype named LIPAc (Linear IFMIF Prototype Accelerator). It is a high intensity deuteron accelerator identical to the low energy part of the IFMIF accelerators. The LIPAc components, which will be installed in Japan, are delivered by different european countries. The accelerator supplies a 9 MeV constant wave beam of deuterons with a power of 1.125 MW, which after being characterized by different instruments has to be stopped safely. For such task a beam dump to absorb the beam energy and take it to a heat sink is needed. Spain has the compromise of delivering such device and CIEMAT (Centro de Investigaciones Energéticas Medioambientales y Tecnológicas) is responsible for such task. The central piece of the beam dump, where the ion beam is stopped, is a copper cone with an angle of 3.5o, 2.5 m long and 5 mm width. This part is cooled by water flowing on its external surface through the channel formed between the copper cone and a concentric piece with the latter. The thesis is developed in this realm, and its objective is designing the LIPAc beam dump cooling system. The design has been performed employing a simplified one dimensional model. The water parameters (pressure, flow, pressure loss) and the required annular channel geometry (width, rugoisty) have been obtained guaranteeing the correct cooling of the beam dump. It has been checked that the cooling design allows variations of the the beam with respect to the nominal position, being the CHF (Critical Heat Flux) at least twice times higher than the nominal deposited heat flux. 3D fluid dynamic simulations employing ANSYS-CFX code in the beam dump cooling channel sections which require a more thorough study have also been performed. The beam dump will activateasaconsequenceofthe deuteron beam interaction, making impossible any change or maintenance task once the accelerator operation has started. Hence the design has to be very robust and all the hypotheses employed in the design mustbecarefully checked. Most of the work in the thesis is concentrated in estimating the heat transfer coefficient which is decisive in the obtained results, and is also employed as boundary condition in the mechanical analysis. For such task, correlations which applicability range is the adequate for the beam dump conditions (annular channel, water-surface temperature differences of tens of degrees) have been compiled. In a second step the heat transfer coefficients obtained from the selected correlation (Petukhov- Gnielinski) have been compared with the ones deduced from the 3D fluid dynamic simulations, obtaining satisfactory results. Finally an experimental validation has been performed employing a prototype and a hydraulic circuit that supplies a flow with the requested parameters in the beam dump. After several tries and improvements in the experiment, the heat transfer coefficients for different flows and heating powers have been obtained. Considering the uncertainty in the measurements the experimental values agree reasonably well (in the order of 15%) with the ones obtained from the correlations. Due to radiological reasons the quality of the cooling water must be controlled, hence minimizing the copper corrosion. After performing a bibligraphic study the most adequate water parameters were identified (conductivity, pH and dissolved oxygen concentration). As part of this thesis a corrosion study of the beam dump cooling circuit has been performed with the double aim of determining if corrosion can pose a risk for the copper beam dump , and obtaining an estimation of the corrosion velocitytodimension the water purification system. TRACT code(TRansport and ACTivation) has been employed for such study adapting the code for the beam dump case. For such study a collaboration with the code responsible (Panos Karditsas) at Culham (UKAEA) was established. The work developed in this thesis has supposed the publication of three articles in JCR journals (”Journal of Nuclear Materials” y ”Fusion Engineering and Design”), as well as presentations in more than four conferences and relevant meetings.

Basics on design and analysis of SE experiments: widespread shortcomings

Keynote speech about experimental design

Study and analysis of the Leap Motion sensor and the Software Development Kit (SDK) for the implementation of visual Human Computer Interfaces

En este proyecto, se presenta un informe técnico sobre la cámara Leap Motion y el Software Development Kit correspondiente, el cual es un dispositivo con una cámara de profundidad orientada a interfaces hombre-máquina. Esto es realizado con el propósito de desarrollar una interfaz hombre-máquina basada en un sistema de reconocimiento de gestos de manos. Después de un exhaustivo estudio de la cámara Leap Motion, se han realizado diversos programas de ejemplo con la intención de verificar las capacidades descritas en el informe técnico, poniendo a prueba la Application Programming Interface y evaluando la precisión de las diferentes medidas obtenidas sobre los datos de la cámara. Finalmente, se desarrolla un prototipo de un sistema de reconocimiento de gestos. Los datos sobre la posición y orientación de la punta de los dedos obtenidos de la Leap Motion son usados para describir un gesto mediante un vector descriptor, el cual es enviado a una Máquina Vectores Soporte, utilizada como clasificador multi-clase.

High-brightness all semiconductor laser at 1.57 µm for space-borne lidar measurements of atmospheric carbon dioxide: device design and analysis of requirements

The availability of suitable laser sources is one of the main challenges in future space missions for accurate measurement of atmospheric CO2. The main objective of the European project BRITESPACE is to demonstrate the feasibility of an all-semiconductor laser source to be used as a space-borne laser transmitter in an Integrated Path Differential Absorption (IPDA) lidar system. We present here the proposed transmitter and system architectures, the initial device design and the results of the simulations performed in order to estimate the source requirements in terms of power, beam quality, and spectral properties to achieve the required measurement accuracy. The laser transmitter is based on two InGaAsP/InP monolithic Master Oscillator Power Amplifiers (MOPAs), providing the ON and OFF wavelengths close to the selected absorption line around 1.57 µm. Each MOPA consists of a frequency stabilized Distributed Feedback (DFB) master oscillator, a modulator section, and a tapered semiconductor amplifier optimized to maximize the optical output power. The design of the space-compliant laser module includes the beam forming optics and the thermoelectric coolers.The proposed system replaces the conventional pulsed source with a modulated continuous wave source using the Random Modulation-Continuous Wave (RM-CW) approach, allowing the designed semiconductor MOPA to be applicable in such applications. The system requirements for obtaining a CO2 retrieval accuracy of 1 ppmv and a spatial resolution of less than 10 meters have been defined. Envelope estimated of the returns indicate that the average power needed is of a few watts and that the main noise source is the ambient noise.

Estudio y análisis para la elaboración de un modelo de certificado de calidad cinegética en España = Study and analysis for the development of a model of hunting quality certificate in Spain

Con esta tesis doctoral se pretende elaborar un modelo de Certificado de Calidad Cinegética independiente, de adhesión voluntaria y aplicable a todo tipo de espacios cinegéticos, de forma que posteriormente pueda convertirse en una metodología que sea empleada como instrumento válido de medición de la Calidad Cinegética y normalizada a través de una familia de Normas aprobadas por un organismo de normalización reconocido a nivel nacional o internacional. En primer lugar, se procedió a la realización de un riguroso y exhaustivo estudio de justificación siguiendo la metodología propuesta por la Norma UNE 66172:2003 IN, Directrices para la justificación y desarrollo de sistemas de gestión (equivalente a la Norma Internacional GUIA ISO/IEC 72:2001). A continuación, se procedió a la identificación y desarrollo de los parámetros de Ordenación Cinegética comunes a cualquier espacio cinegético en España y a la conceptualización de la Calidad Cinegética. Finalmente, se desarrolló un modelo estructurado en nueve Criterios y treinta y cuatro Indicadores de Calidad Cinegética, y un proyecto de familia de Normas para la Certificación de la Calidad Cinegética. ABSTRACT This doctoral thesis aims to produce a model of Hunting Quality Certificate independent, of voluntary adherence and applicable to all types of hunting areas, so that later it can become a methodology to be used as a valid instrument for measuring Hunting Quality and standardized through a family of standards approved by an organization of standardization recognized at a national or an international level. First, we proceeded to carry out a rigorous and comprehensive justification study following the methodology proposed by the UNE 66172: 2003 IN, Guidelines for the justification and development of management systems standards (equivalent to the International Standard GUIA ISO / IEC 72: 2001). Then, we proceeded to the identification and development of Hunting Management parameters common to any hunting area in Spain and the conceptualization of Hunting Quality. Finally, a model structured into nine Criteria and thirty-four Indicators of Hunting Quality and a draft of a family of standards for Hunting Quality Certification were developed.

Occurrence and analysis of selected pharmaceutical compounds in soil from Spanish agricultural fields

This work describes the analysis of 15 pharmaceutical compounds, belonging to different therapeutic classes (anti-inflammatory/analgesics, lipid regulators, antiepileptics, ?-blockers and antidepressants) and with diverse physical?chemical properties, in Spanish soils with different farmland uses. The studied compounds were extracted from soil by ultrasound-assisted extraction (UAE) and determined, after derivatization, by gas chromatography with mass spectrometric detection (GC?MS). The limits of detection (LODs) ranged from 0.14 ng g?1 (naproxen) to 0.65 ng g?1 (amitriptyline). At least two compounds where detected in all samples, being ibuprofen, salicylic acid, and paracetamol, the most frequently detected compounds. The highest levels found in soil were 47 ng g?1 for allopurinol and 37 ng g?1 for salicylic acid. The influence of the type of crop and the sampling area on the levels of pharmaceuticals in soil, as well as their relationship with soil physical?chemical properties, was studied. The frequent and widespread detection of some of these compounds in agricultural soils show a diffuse contamination, although the low levels found do not pose a risk to the environment or the human health.

Identification of the salmonid IL-17A/F1a/b, IL-17A/F2b, IL-17A/F3 and IL-17N genes and analysis of their expression following in vitro stimulation and infection

Date of Acceptance: 15/04/2015

Identification and analysis of the plant peroxisomal targeting signal 1 receptor NtPEX5

Protein translocation into peroxisomes takes place via recognition of a peroxisomal targeting signal present at either the extreme C termini (PTS1) or N termini (PTS2) of matrix proteins. In mammals and yeast, the peroxisomal targeting signal receptor, Pex5p, recognizes the PTS1 consisting of -SKL or variants thereof. Although many plant peroxisomal matrix proteins are transported through the PTS1 pathway, little is known about the PTS1 receptor or any other peroxisome assembly protein from plants. We cloned tobacco (Nicotiana tabacum) cDNAs encoding Pex5p (NtPEX5) based on the protein’s interaction with a PTS1-containing protein in the yeast two-hybrid system. Nucleotide sequence analysis revealed that the tobacco Pex5p contains seven tetratricopeptide repeats and that NtPEX5 shares greater sequence similarity with its homolog from humans than from yeast. Expression of NtPEX5 fusion proteins, consisting of the N-terminal part of yeast Pex5p and the C-terminal region of NtPEX5, in a Saccharomyces cerevisiae pex5 mutant restored protein translocation into peroxisomes. These experiments confirmed the identity of the tobacco protein as a PTS1 receptor and indicated that components of the peroxisomal translocation apparatus are conserved functionally. Two-hybrid assays showed that NtPEX5 interacts with a wide range of PTS1 variants that also interact with the human Pex5p. Interestingly, the C-terminal residues of some of these peptides deviated from the established plant PTS1 consensus sequence. We conclude that there are significant sequence and functional similarities between the plant and human Pex5ps.

Extracellular antigen processing and presentation by immature dendritic cells

In antigen presentation to CD4+ T cells, proteins are degraded to peptide fragments and loaded onto class II MHC molecules in a process involving the peptide exchange factors H-2M (murine) or HLA-DM (human). In many antigen-presenting cells these processes occur in intracellular endosomal compartments, where peptides are generated and loaded onto class II MHC proteins for subsequent transport to the surface and presentation to T cells. Here, we provide evidence for an additional antigen-processing pathway in immature dendritic cells (DC). Immature DC express at the cell surface empty or peptide-receptive class II MHC molecules, as well as H-2M or HLA-DM. Secreted DC proteases act extracellularly to process intact proteins into antigenic peptides. Peptides produced by such activity are efficiently loaded onto cell surface class II MHC molecules. Together these elements comprise an unusual extracellular presentation pathway in which antigen processing and peptide loading can occur entirely outside of the cell.

Hereditary hemochromatosis: Effects of C282Y and H63D mutations on association with β2-microglobulin, intracellular processing, and cell surface expression of the HFE protein in COS-7 cells

Hereditary hemochromatosis (HH) is the most common autosomal recessive disorder known in humans. A candidate gene for HH called HFE has recently been cloned that encodes a novel member of the major histocompatibility complex class I family. Most HH patients are homozygous for a Cys-282→Tyr (C282Y) mutation in HFE gene, which has been shown to disrupt interaction with β2-microglobulin; a second mutation, His-63→Asp (H63D), is enriched in HH patients who are heterozygous for C282Y mutation. The aims of this study were to determine the effects of the C282Y and H63D mutations on the cellular trafficking and degradation of the HFE protein in transfected COS-7 cells. The results indicate that, while the wild-type and H63D HFE proteins associate with β2-microglobulin and are expressed on the cell surface of COS-7 cells, these capabilities are lost by the C282Y HFE protein. We present biochemical and immunofluorescence data that indicate that the C282Y mutant protein: (i) is retained in the endoplasmic reticulum and middle Golgi compartment, (ii) fails to undergo late Golgi processing, and (iii) is subject to accelerated degradation. The block in intracellular transport, accelerated turnover, and failure of the C282Y protein to be presented normally on the cell surface provide a possible basis for impaired function of this mutant protein in HH.

Evidence for a recommended dietary allowance for vitamin C from pharmacokinetics: A comment and analysis

The current recommended dietary allowance (RDA) for vitamin C, as proposed by the Food and Nutrition Board/National Research Council in 1980 and reconfirmed in 1989, is 60 mg daily for nonsmoking adult males. Levine et al. [Levine, M., Conry-Cantilena, C., Wang, Y., Welch, R. W., Washko, P. W., et al. (1996) Proc. Natl. Acad. Sci. USA 93, 3704–3709], based on a study of vitamin C pharmacokinetics in seven healthy men, have now proposed that the RDA should be increased to 200 mg daily. I have examined, in brief, the experimental and conceptual bases for this new recommendation and its implications for public health and nutrition policy and programs. Using, for illustrative purposes only, data extracted from each of two recent dietary surveys of noninstitutionalized adult males living in households in the Netherlands and the United States, it is predicted that the prevalence of intakes inadequate to meet the individual’s own requirement would be about 96% or 84%, respectively, if the criteria of adequacy used for derivation of the 200 mg RDA are accepted. Depending upon the particular average requirement value for ascorbic acid that might be derived from their data, the proposal by Levine et al. would mean a desirable increase in mean intakes in these two populations by as much about 2- to 3-fold. Hence, before an action of this kind is to be recommended, an answer must be sought to the question whether current experimental data including the criteria selected (saturation kinetics) are adequate to establish a new set of requirements for vitamin C, which then carry such profound policy implications. This will require critical assessment of all of the available evidence emerging from laboratory, clinical, and epidemiological studies to determine whether it provides a sufficient rationale for accepting criteria of vitamin C adequacy such as those proposed by Levine et al. and the requirement estimates so derived.

Singular value decomposition for genome-wide expression data processing and modeling

We describe the use of singular value decomposition in transforming genome-wide expression data from genes × arrays space to reduced diagonalized “eigengenes” × “eigenarrays” space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.

Evaluation of total purchasing pilots in England and Scotland and implications for primary care groups in England: personal interviews and analysis of routine data

Objectives: To evaluate the reported achievements of the 52 first wave total purchasing pilot schemes in 1996-7 and the factors associated with these; and to consider the implications of these findings for the development of the proposed primary care groups.