Validation of the burn-up code EVOLCODE 2.0 with PWR experimental data and with a Sensitivity/Uncertainty analysis

A validation of the burn-up simulation system EVOLCODE 2.0 is presented here, involving the experimental measurement of U and Pu isotopes and some fission fragments production ratios after a burn-up of around 30 GWd/tU in a Pressurized Light Water Reactor (PWR). This work provides an in-depth analysis of the validation results, including the possible sources of the uncertainties. An uncertainty analysis based on the sensitivity methodology has been also performed, providing the uncertainties in the isotopic content propagated from the cross sections uncertainties. An improvement of the classical Sensitivity/ Uncertainty (S/U) model has been developed to take into account the implicit dependence of the neutron flux normalization, that is, the effect of the constant power of the reactor. The improved S/U methodology, neglected in this kind of studies, has proven to be an important contribution to the explanation of some simulation-experiment discrepancies for which, in general, the cross section uncertainties are, for the most relevant actinides, an important contributor to the simulation uncertainties, of the same order of magnitude and sometimes even larger than the experimental uncertainties and the experiment- simulation differences. Additionally, some hints for the improvement of the JEFF3.1.1 fission yield library and for the correction of some errata in the experimental data are presented.

High sensitivity biosensors based on shear mode AIN resonators for in liquid operation

El diagnóstico y detección temprana de enfermedades son clave para reducir la tasa de mortalidad, las hospitalizaciones de larga duración y el desaprovechamiento de recursos. En los últimos años se ha impulsado, mediante un aumento de la financiación, el desarrollo de nuevos biosensores de bajo coste capaces de detectar y cuantificar cantidades muy pequeñas de especies biológicas de una forma barata y sencilla. El trabajo presentado en esta Tesis Doctoral describe la investigación llevada a cabo en el desarrollo de sensores gravimétricos basados en resonadores de ondas acústicas de volumen (BAW) de estructura maciza (SMR). Los dispositivos emplean películas delgadas de A1N como material piezoeléctrico y operan en modo de cizalladura, para así poder detectar especies biológicas en medio líquido. El principio de funcionamiento de estos sensores se basa en la variación que experimenta la frecuencia de resonancia al quedar una pequeña masa adherida a su superficie. Necesitan operar en modo de cizalladura para que su resonancia no se atenúe al trabajar en medio líquido, así como ofrecer una superficie capaz de ser funcionalizada específicamente para la especie biológica a detectar. El reto planteado en esta tesis requiere un acercamiento pluridisciplinar al problema que incluye el estudio de los diferentes materiales que constituyen la estructura multicapa que forma un SMR, el diseño y fabricación del dispositivo y del sistema de fluídica, la funcionalización bioquímica de la superficie del sensor, la demostración de la capacidad de detección de especies biológicas y finalmente el diseño y fabricación de la electrónica asociada para la detección de la señal eléctrica. Todas esas tareas han sido abordadas en las distintas etapas del desarrollo de esta tesis y las contribuciones más relevantes se describen en el documento. En el campo de desarrollo de los materiales, se propone un proceso en dos etapas para la pulverización reactiva de capas de A1N que contengan microcristales inclinados capaces de excitar el modo de cizalladura. Se caracteriza la velocidad acústica del modo de cizalladura en todos los materiales que componen la estructura, con el fin de poder obtener un diseño más adecuado del reflector acústico. Se propone un nuevo tipo de material aislante de alta impedancia acústica consistente en capas de W03 pulverizadas que presenta ciertas ventajas tecnológicas frente a las capas convencionales de Ta205. Respecto del diseño del transductor, se estudia la influencia que tienen los con tactos eléctricos extendidos del resonador necesarios para poder adaptar el sistema de fluídica a la estructura. Los resultados indican que es necesario trabajar sobre sustratos aislantes (tanto el soporte como el espejo acústico) para evitar efectos parásitos asociados al uso de capas metálicas bajo los electrodos del resonador que dañan su resonancia. Se analiza la influencia de las diferentes capas del dispositivo en el coeficiente de temperatura de la frecuencia (TCF) del resonador llegando a la conclusión de que las dos últimas capas del reflector acústico afectan significativamente al TCF del SMR, pudiendo reducirse ajusfando adecuadamente sus espesores. De acuerdo con los resultados de estos estudios, se han diseñado finalmente resonadores SMR operando a f .3 GHz en modo de cizalladura, con un área activa de 65000 /xm2, contactos eléctricos que se extienden f .7 mm y factores de calidad en líquido de f 50. Las extensiones eléctricas permiten adaptar el resonador a un sistema de fluídica de metacrilato. Para la detección de especies biológicas se realiza un montaje experimental que permite circular 800 ¡A por la superficie del sensor a través de un circuito cerrado que trabaja a volumen constante. La circulación de soluciones iónicas sobre el sensor descubierto pone de manifiesto que las altas frecuencias de operación previenen los cortocircuitos y por tanto el aislamiento de los electrodos es prescindible. Se desarrolla un protocolo ad-hoc de funcionalización basado en el proceso estándar APTESGlutaraldehído. Se proponen dos alternativas novedosas para la funcionalización de las áreas activas del sensor basadas en el uso de capas de oxidación de Ir02 y su activación a través de un plasma de oxígeno que no daña al dispositivo. Ambos procesos contribuyen a simplificar notablemente la funcionalización de los sensores gravimétricos. Se utilizan anticuerpos y aptámeros como receptores para detectar trombina, anticuerpo monoclonal IgG de ratón y bacteria sonicadas. Una calibración preliminar del sensor con depósitos de capas finas de Si02 de densidad y espesor conocidos permite obtener una sensibilidad de 1800 kHz/pg-cm2 y un límite de detección of 4.2 pg. Finalmente se propone el prototipo de un circuito electrónico de excitación y lectura de bajo coste diseñado empleando teoría de circuitos de microondas. Aunque su diseño y funcionamiento admite mejoras, constituye la última etapa de un sistema completo de bajo coste para el diagnóstico de especies biológicas basado en resonadores SMR de A1N. ABSTRACT Early diagnosis and detection of diseases are essential for reducing mortality rate and preventing long-term hospitalization and waste of resources. These requirements have boosted the efforts and funding on the research of accurate and reliable means for detection and quantification of biological species, also known as biosensors. The work presented in this thesis describes the development and fabrication of gravimetric biosensors based on piezoelectric AlN bulk acoustic wave (BAW) solidly mounted resonators (SMRs) for detection of biological species in liquid media. These type of devices base their sensing principles in the variation that their resonant frequency suffers when a mass is attached to their surface. They need to operate in the shear mode to maintain a strong resonance in liquid and an adequate functionalisation of their sensing area to guarantee that only the targeted molecules cause the shift. The challenges that need to be overcome to achieve piezoelectric BAW resonators for high sensitivity detection in fluids require a multidisciplinary approach, that include the study of the materials involved, the design of the device and the fluidic system, the biochemical functionalisation of the active area, the experimental proof-of-concept with different target species and the design of an electronic readout circuit. All this tasks have been tackled at different stages of the thesis and the relevant contributions are described in the document. In the field of materials, a two-stage sputtering deposition process has been developed to obtain good-quality AlN films with uniformly tilted grains required to excite the shear mode. The shear acoustic velocities of the materials composing the acoustic reflector have been accurately studied to ensure an optimum design of the reflector stack. WO3 sputtered films have been proposed as high acoustic impedance material for insulating acoustic reflectors. They display several technological advantages for the processing of the resonators. Regarding the design, a study of the influence of the electrical extensions necessary to fit a fluidic system on the performance of the devices has been performed. The results indicate that high resistivity substrates and insulating reflectors are necessary to avoid the hindering of the resonance due to the parasitic effects induced by the extensions. The influence of the different layers of the stack on the resultant TCF of the SMRs has also been investigated. The two layers of the reflector closer to the piezoelectric layer have a significant influence on the TCF, which can be reduced by modifying their thicknesses accordingly. The data provided by these studies has led to the final design of the devices, which operate at 1.3 GHz in the shear mode and display an active area of 65000 /xm2 and electrical extensions of 1.7 mm while keeping a Qahear=150 in liquid. The extensions enable to fit a custom-made fluidic system made of methacrylate. To perform the biosensing experiments, an experimental setup with a liquid closed circuit operating at constant flow has been developed. Buffers of ionic characteristics have been tested on non-isolated devices, revealing that high operation frequencies prevent the risk of short circuit. An ad-hoc functionalisation protocol based on the standard APTES - Glutaraldehyde process has been developed. It includes two new processes that simplify the fabrication of the transducers: the use of IrO2 as oxidation layer and its functionalisation through an O2 plasma treatment that does not damage the resonators. Both antibodies and aptamers are used as receptors. In liquid sensing proof-of-concept experiments with thrombin, IgG mouse monoclonal antibody and sonicated bacteria have been displayed. A preliminary calibration of the devices using SiO2 layers reveals a sensitivity of 1800 kHz/pg-cm2 and a limit of detection of 4.2 pg. Finally, a first prototype of a low-cost electronic readout circuit designed using a standard microwave approach has been developed. Although its performance can be significantly improved, it is an effective first approach to the final stage of a portable low-cost diagnostic system based on shear mode AlN SMRs.

Molecular cloning and functional analysis of SUT-1, a sulfate transporter from human high endothelial venules

High endothelial venules (HEV) are specialized postcapillary venules found in lymphoid organs and chronically inflamed tissues that support high levels of lymphocyte extravasation from the blood. One of the major characteristics of HEV endothelial cells (HEVEC) is their capacity to incorporate large amounts of sulfate into sialomucin-type counter-receptors for the lymphocyte homing receptor L-selectin. Here, we show that HEVEC express two functional classes of sulfate transporters defined by their differential sensitivity to the anion-exchanger inhibitor 4,4′-diisothiocyanostilbene-2,2′-disulfonic acid (DIDS), and we report the molecular characterization of a DIDS-resistant sulfate transporter from human HEVEC, designated SUT-1. SUT-1 belongs to the family of Na+-coupled anion transporters and exhibits 40–50% amino acid identity with the rat renal Na+/sulfate cotransporter, NaSi-1, as well as with the human and rat Na+/dicarboxylate cotransporters, NaDC-1/SDCT1 and NaDC-3/SDCT2. Functional expression studies in cRNA-injected Xenopus laevis oocytes showed that SUT-1 mediates high levels of Na+-dependent sulfate transport, which is resistant to DIDS inhibition. The SUT-1 gene mapped to human chromosome 7q33. Northern blotting analysis revealed that SUT-1 exhibits a highly restricted tissue distribution, with abundant expression in placenta. Reverse transcription–PCR analysis indicated that SUT-1 and the diastrophic dysplasia sulfate transporter (DTD), one of the two known human DIDS-sensitive sulfate transporters, are coexpressed in HEVEC. SUT-1 and DTD could correspond, respectively, to the DIDS-resistant and DIDS-sensitive components of sulfate uptake in HEVEC. Together, these results demonstrate that SUT-1 is a distinct human Na+-coupled sulfate transporter, likely to play a major role in sulfate incorporation in HEV.

Transfer of the HIV-1 cyclophilin-binding site to simian immunodeficiency virus from Macaca mulatta can confer both cyclosporin sensitivity and cyclosporin dependence

HIV-1 specifically incorporates the peptidyl prolyl isomerase cyclophilin A (CyPA), the cytosolic receptor for the immunosuppressant cyclosporin A (CsA). HIV-1 replication is inhibited by CsA as well as by nonimmunosuppressive CsA analogues that bind to CyPA and interfere with its virion association. In contrast, the related simian immunodeficiency virus SIVmac, which does not interact with CyPA, is resistant to these compounds. The incorporation of CyPA into HIV-1 virions is mediated by a specific interaction between the active site of the enzyme and the capsid (CA) domain of the HIV-1 Gag polyprotein. We report here that the transfer of HIV-1 CA residues 86–93, which form part of an exposed loop, to the corresponding position in SIVmac resulted in the efficient incorporation of CyPA and conferred an HIV-1-like sensitivity to a nonimmunosuppressive cyclosporin. HIV-1 CA residues 86–90 were also sufficient to transfer the ability to efficiently incorporate CyPA, provided that the length of the CyPA-binding loop was preserved. However, the resulting SIVmac mutant required the presence of cyclosporin for efficient virus replication. The results indicate that the presence or absence of a type II tight turn adjacent to the primary CyPA-binding site determines whether CyPA incorporation enhances or inhibits viral replication. By demonstrating that CyPA-binding-site residues can induce cyclosporin sensitivity in a heterologous context, this study provides direct in vivo evidence that the exposed loop between helices IV and V of HIV-1 CA not merely constitutes a docking site for CyPA but is a functional target of this cellular protein.

A peptide derived from an extracellular domain selectively inhibits receptor internalization: Target sequences on insulin and insulin-like growth factor 1 receptors

Certain peptides derived from the α1 domain of the major histocompatibility class I antigen complex (MHC-I) inhibit receptor internalization, increasing the steady-state number of active receptors on the cell surface and thereby enhancing the sensitivity to hormones and other agonists. These peptides self-assemble, and they also bind to MHC-I at the same site from which they are derived, suggesting that they could bind to receptor sites with significant sequence similarity. Receptors affected by MHC-I peptides do, indeed, have such sequence similarity, as illustrated here by insulin receptor (IR) and insulin-like growth factor-1 receptor. A synthetic peptide with sequence identical to a certain extracellular receptor domain binds to that receptor in a ligand-dependent manner and inhibits receptor internalization. Moreover, each such peptide is selective for its cognate receptor. An antibody to the IR peptide not only binds to IR and competes with the peptide but also inhibits insulin-dependent internalization of IR. These observations, and binding studies with deletion mutants of IR, indicate that the sequence QILKELEESSF encoded by exon 10 plays a key role in IR internalization. Our results illustrate a principle for identifying receptor-specific sites of importance for receptor internalization, and for enhancing sensitivity to hormones and other agonists.

Sensitivity to inhibition by β-chemokines correlates with biological phenotypes of primary HIV-1 isolates

Primary HIV-1 isolates were evaluated for their sensitivity to inhibition by β-chemokines RANTES (regulated upon activation, normal T-cell expressed and secreted), macrophage inflammatory protein 1α (MIP-1α), and MIP-1β. Virus isolates of both nonsyncytium-inducing (NSI) and syncytium-inducing (SI) biological phenotypes recovered from patients at various stages of HIV-1 infection were assessed, and the results indicated that only the isolates with the NSI phenotype were substantially inhibited by the β-chemokines. More important to note, these data demonstrate that resistance to inhibition by β-chemokines RANTES, MIP-1α, and MIP-1β is not restricted to T cell line-adapted SI isolates but is also a consistent property among primary SI isolates. Analysis of isolates obtained sequentially from infected individuals in whom viruses shifted from NSI to SI phenotype during clinical progression exhibited a parallel loss of sensitivity to β-chemokines. Loss of virus sensitivity to inhibition by β-chemokines RANTES, MIP-1α, and MIP-1β was furthermore associated with changes in the third variable (V3) region amino acid residues previously described to correlate with a shift of virus phenotype from NSI to SI. Of interest, an intermediate V3 genotype correlated with a partial inhibition by the β-chemokines. In addition, we also identified viruses sensitive to RANTES, MIP-1α, and MIP-1β of NSI phenotype that were isolated from individuals with AIDS manifestations, indicating that loss of sensitivity to β-chemokine inhibition and shift in viral phenotype are not necessarily prerequisites for the pathogenesis of HIV-1 infection.

Studies on the enzymatic and transcriptional activity of the dimerization cofactor for hepatocyte nuclear factor 1

The relationship between the enzymatic and the transcriptional activity of the bifunctional protein pterin-4a-carbinolamine dehydratase/dimerization cofactor for hepatocyte nuclear factor 1 (DCoH) has been elucidated by site-directed mutagenesis. DCoH dimers harbor a binding site for hepatocyte nuclear factor 1 (HNF1), two active centers that bind pterins, and a saddle-shaped surface that resembles nucleic acid binding domains. Two domains of the protein have been selectively targeted to determine if a change in one activity affects the other. No strong correlation has been found, supporting the idea that carbinolamine dehydratase activity is not required for HNF1 binding in vitro or transcriptional coactivation in vivo. Double mutations in the active center, however, influence the in vivo transcriptional activity but not HNF1 binding. This finding suggests that some active center residues also are used during transcription, possibly for binding of another (macro)molecule. Several mutations in the saddle led to a surprising increase in transcription, therefore linking this domain to transcriptional regulation as well. The transcriptional function of DCoH therefore is composed of two parts, HNF1 binding and another contributing effect that involves the active site and, indirectly, the saddle.

Defective trafficking and function of KATP channels caused by a sulfonylurea receptor 1 mutation associated with persistent hyperinsulinemic hypoglycemia of infancy

The ATP-sensitive potassium channel (KATP) regulates insulin secretion in pancreatic β cells. Loss of functional KATP channels because of mutations in either the SUR1 or Kir6.2 channel subunit causes persistent hyperinsulinemic hypoglycemia of infancy (PHHI). We investigated the molecular mechanism by which a single phenylalanine deletion in SUR1 (ΔF1388) causes PHHI. Previous studies have shown that coexpression of ΔF1388 SUR1 with Kir6.2 results in no channel activity. We demonstrate here that the lack of functional expression is due to failure of the mutant channel to traffic to the cell surface. Trafficking of KATP channels requires that the endoplasmic reticulum-retention signal, RKR, present in both SUR1 and Kir6.2, be shielded during channel assembly. To ask whether ΔF1388 SUR1 forms functional channels with Kir6.2, we inactivated the RKR signal in ΔF1388 SUR1 by mutation to AAA (ΔF1388 SUR1AAA). Inactivation of similar endoplasmic reticulum-retention signals in the cystic fibrosis transmembrane conductance regulator has been shown to partially overcome the trafficking defect of a cystic fibrosis transmembrane conductance regulator mutation, ΔF508. We found that coexpression of ΔF1388 SUR1AAA with Kir6.2 led to partial surface expression of the mutant channel. Moreover, mutant channels were active. Compared with wild-type channels, the mutant channels have reduced ATP sensitivity and do not respond to stimulation by MgADP or diazoxide. The RKR → AAA mutation alone has no effect on channel properties. Our results establish defective trafficking of KATP channels as a molecular basis of PHHI and show that F1388 in SUR1 is critical for normal trafficking and function of KATP channels.

Further Studies of the Role of Cyclic β-Glucans in Symbiosis. An ndvC Mutant of Bradyrhizobium japonicum Synthesizes Cyclodecakis-(1→3)-β-Glucosyl1

The cyclic β-(1→3),β-(1→6)-d-glucan synthesis locus of Bradyrhizobium japonicum is composed of at least two genes, ndvB and ndvC. Mutation in either gene affects glucan synthesis, as well as the ability of the bacterium to establish a successful symbiotic interaction with the legume host soybean (Glycine max). B. japonicum strain AB-14 (ndvB::Tn5) does not synthesize β-glucans, and strain AB-1 (ndvC::Tn5) synthesizes a cyclic β-glucan lacking β-(1→6)-glycosidic bonds. We determined that the structure of the glucan synthesized by strain AB-1 is cyclodecakis-(1→3)-β-d-glucosyl, a cyclic β-(1→3)-linked decasaccharide in which one of the residues is substituted in the 6 position with β-laminaribiose. Cyclodecakis-(1→3)-β-d-glucosyl did not suppress the fungal β-glucan-induced plant defense response in soybean cotyledons and had much lower affinity for the putative membrane receptor protein than cyclic β-(1→3),β-(1→6)-glucans produced by wild-type B. japonicum. This is consistent with the hypothesis presented previously that the wild-type cyclic β-glucans may function as suppressors of a host defense response.

Regulation of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase by Carbamylation and 2-Carboxyarabinitol 1-Phosphate in Tobacco: Insights from Studies of Antisense Plants Containing Reduced Amounts of Rubisco Activase1

The regulation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activity by 2-carboxyarabinitol 1-phosphate (CA1P) was investigated using gas-exchange analysis of antisense tobacco (Nicotiana tabacum) plants containing reduced levels of Rubisco activase. When an increase in light flux from darkness to 1200 μmol quanta m−2 s−1 was followed, the slow increase in CO2 assimilation by antisense leaves contained two phases: one represented the activation of the noncarbamylated form of Rubisco, which was described previously, and the other represented the activation of the CA1P-inhibited form of Rubisco. We present evidence supporting this conclusion, including the observation that this second phase, like CA1P, is only present following darkness or very low light flux. In addition, the second phase of CO2 assimilation was correlated with leaf CA1P content. When this novel phase was resolved from the CO2 assimilation trace, most of it was found to have kinetics similar to the activation of the noncarbamylated form of Rubisco. Additionally, kinetics of the novel phase indicated that the activation of the CA1P-inhibited form of Rubisco proceeds faster than the degradation of CA1P by CA1P phosphatase. These results may be significant with respect to current models of the regulation of Rubisco activity by Rubisco activase.

Sensitivity to abscisic acid of guard-cell K+ channels is suppressed by abi1-1, a mutant Arabidopsis gene encoding a putative protein phosphatase.

Abscisic acid (ABA) modulates the activities of three major classes of ion channels--inward- and outward-rectifying K+ channels (IK,in and IK,out, respectively) and anion channels--at the guard-cell plasma membrane to achieve a net efflux of osmotica and stomatal closure. Disruption of ABA sensitivity in wilty abi1-1 mutants of Arabidopsis and evidence that this gene encodes a protein phosphatase suggest that protein (de)-phosphorylation contributes to guard-cell transport control by ABA. To pinpoint the role of ABI1, the abi1-1 dominant mutant allele was stably transformed into Nicotiana benthamiana and its influence on IK,in, IK,out, and the anion channels was monitored in guard cells under voltage clamp. Compared with guard cells from wild-type and vector-transformed control plants, expression of the abi1-1 gene was associated with 2- to 6-fold reductions in IK,out and an insensitivity of both IK,in and IK,out to 20 microM ABA. In contrast, no differences between control and abi1-1 transgenic plants were observed in the anion current or its response to ABA. Parallel measurements of intracellular pH (pHi) using the fluorescent dye 2',7'-bis(2-carboxyethyl)-5-(and -6)-carboxyfluorescein (BCECF) in every case showed a 0.15- to 0.2-pH-unit alkalinization in ABA, demonstrating that the transgene was without effect on the pHi signal that mediates in ABA-evoked K+ channel control. In guard cells from the abi1-1 transformants, normal sensitivity of both K+ channels to and stomatal closure in ABA was recovered in the presence of 100 microM H7 and 0.5 microM staurosporine, both broad-range protein kinase antagonists. These results demonstrate an aberrant K+ channel behavior--including channel insensitivity to ABA-dependent alkalinization of pHi--as a major consequence of abi1-1 action and implicate AB11 as part of a phosphatase/kinase pathway that modulates the sensitivity of guard-cell K+ channels to ABA-evoked signal cascades.

Studies of the lamin proteinase reveal multiple parallel biochemical pathways during apoptotic execution.

Although specific proteinases play a critical role in the active phase of apoptosis, their substrates are largely unknown. We previously identified poly(ADP-ribose) polymerase (PARP) as an apoptosis-associated substrate for proteinase(s) related to interleukin 1 beta-converting enzyme (ICE). Now we have used a cell-free system to characterize proteinase(s) that cleave the nuclear lamins during apoptosis. Lamin cleavage during apoptosis requires the action of a second ICE-like enyzme, which exhibits kinetics of cleavage and a profile of sensitivity to specific inhibitors that is distinct from the PARP proteinase. Thus, multiple ICE-like enzymes are required for apoptotic events in these cell-free extracts. Inhibition of the lamin proteinase with tosyllysine "chloromethyl ketone" blocks nuclear apoptosis prior to the packaging of condensed chromatin into apoptotic bodies. Under these conditions, the nuclear DNA is fully cleaved to a nucleosomal ladder. Our studies reveal that the lamin proteinase and the fragmentation nuclease function in independent parallel pathways during the final stages of apoptotic execution. Neither pathway alone is sufficient for completion of nuclear apoptosis. Instead, the various activities cooperate to drive the disassembly of the nucleus.