Contribución al estudio de las metodologías de cálculo realista con incertidumbre (BEPU), dentro del análisis determinista de seguridad de plantas nucleares

El análisis determinista de seguridad (DSA) es el procedimiento que sirve para diseñar sistemas, estructuras y componentes relacionados con la seguridad en las plantas nucleares. El DSA se basa en simulaciones computacionales de una serie de hipotéticos accidentes representativos de la instalación, llamados escenarios base de diseño (DBS). Los organismos reguladores señalan una serie de magnitudes de seguridad que deben calcularse en las simulaciones, y establecen unos criterios reguladores de aceptación (CRA), que son restricciones que deben cumplir los valores de esas magnitudes. Las metodologías para realizar los DSA pueden ser de 2 tipos: conservadoras o realistas. Las metodologías conservadoras utilizan modelos predictivos e hipótesis marcadamente pesimistas, y, por ello, relativamente simples. No necesitan incluir un análisis de incertidumbre de sus resultados. Las metodologías realistas se basan en hipótesis y modelos predictivos realistas, generalmente mecanicistas, y se suplementan con un análisis de incertidumbre de sus principales resultados. Se les denomina también metodologías BEPU (“Best Estimate Plus Uncertainty”). En ellas, la incertidumbre se representa, básicamente, de manera probabilista. Para metodologías conservadores, los CRA son, simplemente, restricciones sobre valores calculados de las magnitudes de seguridad, que deben quedar confinados en una “región de aceptación” de su recorrido. Para metodologías BEPU, el CRA no puede ser tan sencillo, porque las magnitudes de seguridad son ahora variables inciertas. En la tesis se desarrolla la manera de introducción de la incertidumbre en los CRA. Básicamente, se mantiene el confinamiento a la misma región de aceptación, establecida por el regulador. Pero no se exige el cumplimiento estricto sino un alto nivel de certidumbre. En el formalismo adoptado, se entiende por ello un “alto nivel de probabilidad”, y ésta corresponde a la incertidumbre de cálculo de las magnitudes de seguridad. Tal incertidumbre puede considerarse como originada en los inputs al modelo de cálculo, y propagada a través de dicho modelo. Los inputs inciertos incluyen las condiciones iniciales y de frontera al cálculo, y los parámetros empíricos de modelo, que se utilizan para incorporar la incertidumbre debida a la imperfección del modelo. Se exige, por tanto, el cumplimiento del CRA con una probabilidad no menor a un valor P0 cercano a 1 y definido por el regulador (nivel de probabilidad o cobertura). Sin embargo, la de cálculo de la magnitud no es la única incertidumbre existente. Aunque un modelo (sus ecuaciones básicas) se conozca a la perfección, la aplicación input-output que produce se conoce de manera imperfecta (salvo que el modelo sea muy simple). La incertidumbre debida la ignorancia sobre la acción del modelo se denomina epistémica; también se puede decir que es incertidumbre respecto a la propagación. La consecuencia es que la probabilidad de cumplimiento del CRA no se puede conocer a la perfección; es una magnitud incierta. Y así se justifica otro término usado aquí para esta incertidumbre epistémica: metaincertidumbre. Los CRA deben incorporar los dos tipos de incertidumbre: la de cálculo de la magnitud de seguridad (aquí llamada aleatoria) y la de cálculo de la probabilidad (llamada epistémica o metaincertidumbre). Ambas incertidumbres pueden introducirse de dos maneras: separadas o combinadas. En ambos casos, el CRA se convierte en un criterio probabilista. Si se separan incertidumbres, se utiliza una probabilidad de segundo orden; si se combinan, se utiliza una probabilidad única. Si se emplea la probabilidad de segundo orden, es necesario que el regulador imponga un segundo nivel de cumplimiento, referido a la incertidumbre epistémica. Se denomina nivel regulador de confianza, y debe ser un número cercano a 1. Al par formado por los dos niveles reguladores (de probabilidad y de confianza) se le llama nivel regulador de tolerancia. En la Tesis se razona que la mejor manera de construir el CRA BEPU es separando las incertidumbres, por dos motivos. Primero, los expertos defienden el tratamiento por separado de incertidumbre aleatoria y epistémica. Segundo, el CRA separado es (salvo en casos excepcionales) más conservador que el CRA combinado. El CRA BEPU no es otra cosa que una hipótesis sobre una distribución de probabilidad, y su comprobación se realiza de forma estadística. En la tesis, los métodos estadísticos para comprobar el CRA BEPU en 3 categorías, según estén basados en construcción de regiones de tolerancia, en estimaciones de cuantiles o en estimaciones de probabilidades (ya sea de cumplimiento, ya sea de excedencia de límites reguladores). Según denominación propuesta recientemente, las dos primeras categorías corresponden a los métodos Q, y la tercera, a los métodos P. El propósito de la clasificación no es hacer un inventario de los distintos métodos en cada categoría, que son muy numerosos y variados, sino de relacionar las distintas categorías y citar los métodos más utilizados y los mejor considerados desde el punto de vista regulador. Se hace mención especial del método más utilizado hasta el momento: el método no paramétrico de Wilks, junto con su extensión, hecha por Wald, al caso multidimensional. Se decribe su método P homólogo, el intervalo de Clopper-Pearson, típicamente ignorado en el ámbito BEPU. En este contexto, se menciona el problema del coste computacional del análisis de incertidumbre. Los métodos de Wilks, Wald y Clopper-Pearson requieren que la muestra aleatortia utilizada tenga un tamaño mínimo, tanto mayor cuanto mayor el nivel de tolerancia exigido. El tamaño de muestra es un indicador del coste computacional, porque cada elemento muestral es un valor de la magnitud de seguridad, que requiere un cálculo con modelos predictivos. Se hace especial énfasis en el coste computacional cuando la magnitud de seguridad es multidimensional; es decir, cuando el CRA es un criterio múltiple. Se demuestra que, cuando las distintas componentes de la magnitud se obtienen de un mismo cálculo, el carácter multidimensional no introduce ningún coste computacional adicional. Se prueba así la falsedad de una creencia habitual en el ámbito BEPU: que el problema multidimensional sólo es atacable desde la extensión de Wald, que tiene un coste de computación creciente con la dimensión del problema. En el caso (que se da a veces) en que cada componente de la magnitud se calcula independientemente de los demás, la influencia de la dimensión en el coste no se puede evitar. Las primeras metodologías BEPU hacían la propagación de incertidumbres a través de un modelo sustitutivo (metamodelo o emulador) del modelo predictivo o código. El objetivo del metamodelo no es su capacidad predictiva, muy inferior a la del modelo original, sino reemplazar a éste exclusivamente en la propagación de incertidumbres. Para ello, el metamodelo se debe construir con los parámetros de input que más contribuyan a la incertidumbre del resultado, y eso requiere un análisis de importancia o de sensibilidad previo. Por su simplicidad, el modelo sustitutivo apenas supone coste computacional, y puede estudiarse exhaustivamente, por ejemplo mediante muestras aleatorias. En consecuencia, la incertidumbre epistémica o metaincertidumbre desaparece, y el criterio BEPU para metamodelos se convierte en una probabilidad simple. En un resumen rápido, el regulador aceptará con más facilidad los métodos estadísticos que menos hipótesis necesiten; los exactos más que los aproximados; los no paramétricos más que los paramétricos, y los frecuentistas más que los bayesianos. El criterio BEPU se basa en una probabilidad de segundo orden. La probabilidad de que las magnitudes de seguridad estén en la región de aceptación no sólo puede asimilarse a una probabilidad de éxito o un grado de cumplimiento del CRA. También tiene una interpretación métrica: representa una distancia (dentro del recorrido de las magnitudes) desde la magnitud calculada hasta los límites reguladores de aceptación. Esta interpretación da pie a una definición que propone esta tesis: la de margen de seguridad probabilista. Dada una magnitud de seguridad escalar con un límite superior de aceptación, se define el margen de seguridad (MS) entre dos valores A y B de la misma como la probabilidad de que A sea menor que B, obtenida a partir de las incertidumbres de A y B. La definición probabilista de MS tiene varias ventajas: es adimensional, puede combinarse de acuerdo con las leyes de la probabilidad y es fácilmente generalizable a varias dimensiones. Además, no cumple la propiedad simétrica. El término margen de seguridad puede aplicarse a distintas situaciones: distancia de una magnitud calculada a un límite regulador (margen de licencia); distancia del valor real de la magnitud a su valor calculado (margen analítico); distancia desde un límite regulador hasta el valor umbral de daño a una barrera (margen de barrera). Esta idea de representar distancias (en el recorrido de magnitudes de seguridad) mediante probabilidades puede aplicarse al estudio del conservadurismo. El margen analítico puede interpretarse como el grado de conservadurismo (GC) de la metodología de cálculo. Utilizando la probabilidad, se puede cuantificar el conservadurismo de límites de tolerancia de una magnitud, y se pueden establecer indicadores de conservadurismo que sirvan para comparar diferentes métodos de construcción de límites y regiones de tolerancia. Un tópico que nunca se abordado de manera rigurosa es el de la validación de metodologías BEPU. Como cualquier otro instrumento de cálculo, una metodología, antes de poder aplicarse a análisis de licencia, tiene que validarse, mediante la comparación entre sus predicciones y valores reales de las magnitudes de seguridad. Tal comparación sólo puede hacerse en escenarios de accidente para los que existan valores medidos de las magnitudes de seguridad, y eso ocurre, básicamente en instalaciones experimentales. El objetivo último del establecimiento de los CRA consiste en verificar que se cumplen para los valores reales de las magnitudes de seguridad, y no sólo para sus valores calculados. En la tesis se demuestra que una condición suficiente para este objetivo último es la conjunción del cumplimiento de 2 criterios: el CRA BEPU de licencia y un criterio análogo, pero aplicado a validación. Y el criterio de validación debe demostrarse en escenarios experimentales y extrapolarse a plantas nucleares. El criterio de licencia exige un valor mínimo (P0) del margen probabilista de licencia; el criterio de validación exige un valor mínimo del margen analítico (el GC). Esos niveles mínimos son básicamente complementarios; cuanto mayor uno, menor el otro. La práctica reguladora actual impone un valor alto al margen de licencia, y eso supone que el GC exigido es pequeño. Adoptar valores menores para P0 supone menor exigencia sobre el cumplimiento del CRA, y, en cambio, más exigencia sobre el GC de la metodología. Y es importante destacar que cuanto mayor sea el valor mínimo del margen (de licencia o analítico) mayor es el coste computacional para demostrarlo. Así que los esfuerzos computacionales también son complementarios: si uno de los niveles es alto (lo que aumenta la exigencia en el cumplimiento del criterio) aumenta el coste computacional. Si se adopta un valor medio de P0, el GC exigido también es medio, con lo que la metodología no tiene que ser muy conservadora, y el coste computacional total (licencia más validación) puede optimizarse. ABSTRACT Deterministic Safety Analysis (DSA) is the procedure used in the design of safety-related systems, structures and components of nuclear power plants (NPPs). DSA is based on computational simulations of a set of hypothetical accidents of the plant, named Design Basis Scenarios (DBS). Nuclear regulatory authorities require the calculation of a set of safety magnitudes, and define the regulatory acceptance criteria (RAC) that must be fulfilled by them. Methodologies for performing DSA van be categorized as conservative or realistic. Conservative methodologies make use of pessimistic model and assumptions, and are relatively simple. They do not need an uncertainty analysis of their results. Realistic methodologies are based on realistic (usually mechanistic) predictive models and assumptions, and need to be supplemented with uncertainty analyses of their results. They are also termed BEPU (“Best Estimate Plus Uncertainty”) methodologies, and are typically based on a probabilistic representation of the uncertainty. For conservative methodologies, the RAC are simply the restriction of calculated values of safety magnitudes to “acceptance regions” defined on their range. For BEPU methodologies, the RAC cannot be so simple, because the safety magnitudes are now uncertain. In the present Thesis, the inclusion of uncertainty in RAC is studied. Basically, the restriction to the acceptance region must be fulfilled “with a high certainty level”. Specifically, a high probability of fulfillment is required. The calculation uncertainty of the magnitudes is considered as propagated from inputs through the predictive model. Uncertain inputs include model empirical parameters, which store the uncertainty due to the model imperfection. The fulfillment of the RAC is required with a probability not less than a value P0 close to 1 and defined by the regulator (probability or coverage level). Calculation uncertainty is not the only one involved. Even if a model (i.e. the basic equations) is perfectly known, the input-output mapping produced by the model is imperfectly known (unless the model is very simple). This ignorance is called epistemic uncertainty, and it is associated to the process of propagation). In fact, it is propagated to the probability of fulfilling the RAC. Another term used on the Thesis for this epistemic uncertainty is metauncertainty. The RAC must include the two types of uncertainty: one for the calculation of the magnitude (aleatory uncertainty); the other one, for the calculation of the probability (epistemic uncertainty). The two uncertainties can be taken into account in a separate fashion, or can be combined. In any case the RAC becomes a probabilistic criterion. If uncertainties are separated, a second-order probability is used; of both are combined, a single probability is used. On the first case, the regulator must define a level of fulfillment for the epistemic uncertainty, termed regulatory confidence level, as a value close to 1. The pair of regulatory levels (probability and confidence) is termed the regulatory tolerance level. The Thesis concludes that the adequate way of setting the BEPU RAC is by separating the uncertainties. There are two reasons to do so: experts recommend the separation of aleatory and epistemic uncertainty; and the separated RAC is in general more conservative than the joint RAC. The BEPU RAC is a hypothesis on a probability distribution, and must be statistically tested. The Thesis classifies the statistical methods to verify the RAC fulfillment in 3 categories: methods based on tolerance regions, in quantile estimators and on probability (of success or failure) estimators. The former two have been termed Q-methods, whereas those in the third category are termed P-methods. The purpose of our categorization is not to make an exhaustive survey of the very numerous existing methods. Rather, the goal is to relate the three categories and examine the most used methods from a regulatory standpoint. Special mention deserves the most used method, due to Wilks, and its extension to multidimensional variables (due to Wald). The counterpart P-method of Wilks’ is Clopper-Pearson interval, typically ignored in the BEPU realm. The problem of the computational cost of an uncertainty analysis is tackled. Wilks’, Wald’s and Clopper-Pearson methods require a minimum sample size, which is a growing function of the tolerance level. The sample size is an indicator of the computational cost, because each element of the sample must be calculated with the predictive models (codes). When the RAC is a multiple criteria, the safety magnitude becomes multidimensional. When all its components are output of the same calculation, the multidimensional character does not introduce additional computational cost. In this way, an extended idea in the BEPU realm, stating that the multi-D problem can only be tackled with the Wald extension, is proven to be false. When the components of the magnitude are independently calculated, the influence of the problem dimension on the cost cannot be avoided. The former BEPU methodologies performed the uncertainty propagation through a surrogate model of the code, also termed emulator or metamodel. The goal of a metamodel is not the predictive capability, clearly worse to the original code, but the capacity to propagate uncertainties with a lower computational cost. The emulator must contain the input parameters contributing the most to the output uncertainty, and this requires a previous importance analysis. The surrogate model is practically inexpensive to run, so that it can be exhaustively analyzed through Monte Carlo. Therefore, the epistemic uncertainty due to sampling will be reduced to almost zero, and the BEPU RAC for metamodels includes a simple probability. The regulatory authority will tend to accept the use of statistical methods which need a minimum of assumptions: exact, nonparametric and frequentist methods rather than approximate, parametric and bayesian methods, respectively. The BEPU RAC is based on a second-order probability. The probability of the safety magnitudes being inside the acceptance region is a success probability and can be interpreted as a fulfillment degree if the RAC. Furthermore, it has a metric interpretation, as a distance (in the range of magnitudes) from calculated values of the magnitudes to acceptance regulatory limits. A probabilistic definition of safety margin (SM) is proposed in the thesis. The same from a value A to other value B of a safety magnitude is defined as the probability that A is less severe than B, obtained from the uncertainties if A and B. The probabilistic definition of SM has several advantages: it is nondimensional, ranges in the interval (0,1) and can be easily generalized to multiple dimensions. Furthermore, probabilistic SM are combined according to the probability laws. And a basic property: probabilistic SM are not symmetric. There are several types of SM: distance from a calculated value to a regulatory limit (licensing margin); or from the real value to the calculated value of a magnitude (analytical margin); or from the regulatory limit to the damage threshold (barrier margin). These representations of distances (in the magnitudes’ range) as probabilities can be applied to the quantification of conservativeness. Analytical margins can be interpreted as the degree of conservativeness (DG) of the computational methodology. Conservativeness indicators are established in the Thesis, useful in the comparison of different methods of constructing tolerance limits and regions. There is a topic which has not been rigorously tackled to the date: the validation of BEPU methodologies. Before being applied in licensing, methodologies must be validated, on the basis of comparisons of their predictions ad real values of the safety magnitudes. Real data are obtained, basically, in experimental facilities. The ultimate goal of establishing RAC is to verify that real values (aside from calculated values) fulfill them. In the Thesis it is proved that a sufficient condition for this goal is the conjunction of 2 criteria: the BEPU RAC and an analogous criterion for validation. And this las criterion must be proved in experimental scenarios and extrapolated to NPPs. The licensing RAC requires a minimum value (P0) of the probabilistic licensing margin; the validation criterion requires a minimum value of the analytical margin (i.e., of the DG). These minimum values are basically complementary; the higher one of them, the lower the other one. The regulatory practice sets a high value on the licensing margin, so that the required DG is low. The possible adoption of lower values for P0 would imply weaker exigence on the RCA fulfillment and, on the other hand, higher exigence on the conservativeness of the methodology. It is important to highlight that a higher minimum value of the licensing or analytical margin requires a higher computational cost. Therefore, the computational efforts are also complementary. If medium levels are adopted, the required DG is also medium, and the methodology does not need to be very conservative. The total computational effort (licensing plus validation) could be optimized.

Estructura espacial y dinámica del bosque montano del sur del Ecuador. Interacciones bióticas y limitaciones abióticas

Muchos estudios han descrito la composición y diversidad de los bosques montanos tropicales, pero los patrones espaciales y las diferentes tipos de relaciones de estos, entre especies o entre grupos funcionales ha sido poco documentada. El presente trabajo se realizó en tres parcelas completamente censadas del bosque de la Estación Biológica “Chamusquin” (Zamora Chinchipe, Ecuador), y se plantea como objetivo principal conocer la estructura espacial y dinámica del bosque montano tropical del sur del Ecuador, así como las interacciones bióticas y limitaciones abióticas que influyen en esta dinámica, para ello se planteó cuatro objetivos de estudio que son: conocer los patrones espaciales de los gremios ecológicos dentro de la zona de estudio; conocer la influencia de la dependencia negativa de la densidad sobre dos especies de helechos arborescentes (Cyatheaceae); conocer si existen especies o grupos ecológicos acumuladoras o repulsoras de diversidad en el área de estudio; y conocer cómo influyen la diversidad filogenética y la densidad del vecindario en la incidencia de herbivoría y parasitismo sobre las fases iniciales del establecimiento forestal (brinzales) así como en la supervivencia de los mismos Como paso previo para el análisis del resto de objetivos, dentro de cada parcela se marcaron todos los individuos con DAP ≥5 cm y se tomaron sus coordenadas (X, Y). Además se tomaron datos de variables superficiales y muestras del suelo. Las especies encontradas se clasificaron de acuerdo a sus características biológicas, asignándolas a cada uno de los cuatro gremios forestales usualmente distinguidos en los bosques tropicales: tolerantes a la sombra (TS), tolerantes parciales a la sombra (TPS), pioneras de vida larga (PVL) y pioneras de vida corta (PVC). Para el estudio del primer objetivo tas se emplearon funciones K de Ripley inhomogéneas, ajustando la heterogeneidad en base a la variación espacial de las variables ambientales registradas . Los resultados demostraron que tanto la frecuencia relativa como el patrón espacial de las diferentes estrategias funcionales varían a lo largo de la sucesión y que éste además está influido por la variación ambiental. En adición, tanto el patrón espacial como la respuesta a la variación ambiental de los diferentes gremios es distinta entre adultos y juveniles. Todo ello sugiere que el ensamblaje de la diversidad en los bosque montanos andinos está controlado por procesos deterministas más que por procesos neutrales. Para responder el segundo objetivo se estudiaron los efectos de la dependencia negativa de la densidad (DND) y la heterogeneidad ambiental en las poblaciones de dos especies de helechos arborescentes abundantes, Cyathea caracasana y Alsophila engelii, y cómo estos efectos cambian a través de un gradiente sucesional. Los patrones de especies albergan información sobre procesos tales como la competencia que puede ser revelado fácilmente utilizando técnicas de análisis de patrones punto. Sin embargo, su detección puede ser difícil debido a los efectos de factores de confusión heterogeneidad del hábitat. Aquí, empleamos funciones K y funciones de correlación de par homogéneas y no homogéneas para cuantificar el cambio en el patrón espacial de diferentes clases de tamaño con un diseño de casos-controles para estudiar las asociaciones entre helechos arborescentes jóvenes y adultos. Usando estimaciones espaciales de la biomasa de los cuatro tipos de gremios ecológicos (PVC, PVL, TPS, TS) como covariables, hemos ajustado modelos de Poisson heterogéneos a los patrones de puntos de de los helechos juveniles y los adultos y hemos explorado además la existencia de dependencia del hábitat en estos patrones. Nuestro estudio reveló efectos de la DND para C. caracasana y un fuerte filtrado ambiental que subyace al patrón de A. engelii. Encontramos también que las poblaciones de adultos y juveniles de ambas especies respondieron de manera diferente a la heterogeneidad del hábitat y en la mayoría de los casos esta heterogeneidad se asoció con la distribución espacial de la biomasa de los cuatro tipos de gremios. Estos resultados muestran la eficacia de controlar los efectos de la heterogeneidad ambiental para evitar su confusión con los patrones derivados de interacciones biológicas cuando se estudia la DND y demuestran la utilidad de los mapas de covariables derivados de comunidades biológicas como resumen de la heterogeneidad ambiental. Para nuestro tercer objetivo nos centramos en explorar cómo influyen las especies más abundantes en la organización espacial de la diversidad a lo largo de un gradiente sucesional en el bosque montano del sur del Ecuador. Para ello utilizamos la función ISAR (Individual Species Area Relationship). Encontramos que la frecuencia de especies neutras, repulsoras y acumuladoras de diversidad taxonómica varía dependiendo del grado de sucesión. Además se comprobó que la mayoría de los gremios forestales se comportó de forma neutral, pero la proporción de acumuladores, aumentó al avanzar la sucesión hacia estados más maduros, lo que indica el establecimiento de fuertes procesos competitivos a medida que avanza la sucesión y la mayor importancia del papel de las especies individuales en dichos estados. Finalmente, examinamos el efecto de la vecindad taxonómica y filogenética, así como la estrategia de vida, sobre la incidencia de la herbivoría y el parasitismo en las poblaciones de brinzales de tres fragmentos forestales en una secuencia sucesional del bosque montano húmedo. Evaluamos además los efectos de herbivoría, parasitismo, estrategia de vida y diferentes indicadores de la vecindad sobre la supervivencia de los brinzales. Por último contrastamos la posible existencia de una tendencia compensatoria de la comunidad (CCT) a nivel de fragmento forestal. Nuestros análisis no consiguieron detectar una CCT pero si pusieron de manifiesto la existencia de efectos locales de dependencia negativa de la densidad. Por ejemplo, la presencia de herbivoría y parasitismo sobre los brinzales se relacionó significativamente con una menor supervivencia de estos. Por otro lado, indicadores del efecto de la vecindad como la densidad de brinzales del mismo género y el área basal de árboles vecinos del mismo género incrementaron la prevalencia de la herbivoría o el parasitismo en los brinzales. El incremento de la incidencia de la herbivoría o el parasitismo no está exclusivamente ligado a tener una vecindad taxonómicamente idéntica (vecinos de la misma especie) sino que categorías taxonómicas más laxas como el "género" o simplemente relaciones de semejanza filogenética son capaces de predecir los efectos negativos de la vecindad. Los efectos detectados variaron en los diferentes grupos funcionales distinguidos. Los resultados que hemos obtenido en este trabajo parecen indicar que el funcionamiento de las comunidades de brinzales del bosque montano tropical no difiere mucho del reportado para comunidades de plántulas en otros bosques tropicales y cumple las predicciones de la hipótesis de Janzen y Connell, aunque matizadas por la mayor resistencia de los brinzales al efecto de herbivoría y parasitismo. ABSTRACT Many studies have described the composition and diversity of tropical montane forests, but the different spatial patterns and types of relationships between species or between functional groups has been poorly documented. This work was made in three completely surveyed forest plots at Biological Station "Chamusquin" (Zamora Chinchipe, Ecuador). Our main objective was to know the spatial structure and dynamics of the tropical montane forest in southern Ecuador, as well as the biotic interactions and abiotic constraints affecting this dynamic. More specifically, we aimed to understand the spatial patterns of ecological guilds; to explore the influence of negative density dependence on two species of tree ferns (Cyatheaceae); to determine whether some species or ecological groups structure spatially plant diversity in these forests; and to test the effects of biological neighborhood on the incidence of herbivory and parasitism and on the survival of saplings. We mapped within each plot all trees with DBH ≥5 cm. Besides, surface data variables and soil samples they were taken. The species found were classified according to their biological characteristics in four forest guilds: shade-tolerant (ST), partial shade tolerant (PST), long-lived pioneer (LLP) and short-lived pioneer (SLP). To analyze the spatial patterns of the ecological guilds, we employed the inhomogeneous version of Ripley's K-function and adjusted heterogeneity surfaces based on the spatial variation of the measured environmental variables. The results showed that both the relative frequency of each functional guild as well as their spatial pattern varied throughout succession and that the spatial pattern is explained by environmental variation. In addition, both spatial pattern and the response to spatial variation of each guild varied throughout ontogeny. All in all suggest that diversity assembly in the studied forests is ruled by deterministic instead of neutral processes. We also addressed the negative effects of density dependence (NDD) and environmental heterogeneity in populations of two species of abundant tree ferns, Cyathea caracasana and Alsophila engelii, and how these effects change across a successional gradient.. Here, we used homogeneous and inhomogeneous K and pair-correlation functions to quantify the change in the spatial pattern of different size classes with a case-control design to study associations between young and adult tree ferns. Using spatial estimates of the biomass of the four types of ecological guilds (SLP, LLP, PST, ST) as co-variables, we fitted heterogeneous Poisson models to juvenile and adult tree fern point patterns and explored the existence of habitat dependence. Our study revealed NDD effects for C. caracasana and strong environmental filtering underlying the pattern of A. engelii. We found that adult and juvenile populations of both species responded differently to habitat heterogeneity and in most cases this heterogeneity was associated with the spatial distribution of biomass of the four functional tree types. These findings show the effectiveness of factoring out environmental heterogeneity to avoid confounding factors when studying NDD and demonstrate the usefulness of covariate maps derived from mapped communities. For our third objective we focused on exploring how the most abundant species influence the spatial organization of tree diversity in these forests. For this, we used the individual species-area relationship function (ISAR). We found that the proportion of accumulator, repeller and neutral species, varied depending on the degree of succession. We found also that most guilds behaved neutrally but the proportion of accumulator guilds increased as succession advanced to more mature stages. This point, to the existence of strong competitive effects mediated by individual species in these mature forests. Finally, we examined the effects of life strategies and taxonomic and phylogenetic neighborhood on the incidence of herbivory and parasitism in the communities of saplings in the same forest fragments. We evaluated also the effects of life strategies, herbivory, parasitism and some indicators of neighborhood on sapling survival. Finally we tested for the existences of a compensatory community trend at plot scale. We did not found a CCT but we found proof of local NND effects. For instance, the prevalence of herbivory and parasitism were related to lower sapling survival. On the other hand the density of con-generic saplings and the basal area of neighbor con-generic trees were related to a higher prevalence of herbivory or parasitism in the saplings. We demonstrated that the increase in the prevalence of herbivory or parasitism it s not exclusive of a conspecific neighborhood but instead larger taxonomic categories such as "genus" or simple phylogenetic relationships are also able to predict NND effects. The NND effects varied among functional guilds. Our results show that the dynamic of sapling communities in Ecuadorian montane forests is similar to seedling dynamics in other tropical forest and follows the predictions of Janzen-Connell hypothesis, although softened by the strong resilience of saplings in comparison to seedlings.

Folding protein models with a simple hydrophobic energy function: The fundamental importance of monomer inside/outside segregation

The present study explores a “hydrophobic” energy function for folding simulations of the protein lattice model. The contribution of each monomer to conformational energy is the product of its “hydrophobicity” and the number of contacts it makes, i.e., E(h⃗, c⃗) = −Σi=1N cihi = −(h⃗.c⃗) is the negative scalar product between two vectors in N-dimensional cartesian space: h⃗ = (h1, … , hN), which represents monomer hydrophobicities and is sequence-dependent; and c⃗ = (c1, … , cN), which represents the number of contacts made by each monomer and is conformation-dependent. A simple theoretical analysis shows that restrictions are imposed concomitantly on both sequences and native structures if the stability criterion for protein-like behavior is to be satisfied. Given a conformation with vector c⃗, the best sequence is a vector h⃗ on the direction upon which the projection of c⃗ − c̄⃗ is maximal, where c̄⃗ is the diagonal vector with components equal to c̄, the average number of contacts per monomer in the unfolded state. Best native conformations are suggested to be not maximally compact, as assumed in many studies, but the ones with largest variance of contacts among its monomers, i.e., with monomers tending to occupy completely buried or completely exposed positions. This inside/outside segregation is reflected on an apolar/polar distribution on the corresponding sequence. Monte Carlo simulations in two dimensions corroborate this general scheme. Sequences targeted to conformations with large contact variances folded cooperatively with thermodynamics of a two-state transition. Sequences targeted to maximally compact conformations, which have lower contact variance, were either found to have degenerate ground state or to fold with much lower cooperativity.

The Function of Fish Cytokines

Peer reviewed

Microbes as engines of ecosystem function : When does community structure enhance predictions of ecosystem processes?

Peer reviewed

A pair of adjacent glucocorticoid response elements regulate expression of two mouse metallothionein genes

Synthesis of mouse metallothionein (MT)-I and MT-II is transcriptionally induced by the synthetic glucocorticoid, dexamethasone (DEX) or both in vivo as well as in numerous cell lines. However, the location(s) of a glucocorticoid response element (GRE) has not been described. The observation that a marked MT-I gene, as well as heterologous genes, when placed in the context of 17 kb of flanking sequence from the MT locus, are inducible by DEX and lipopolysaccharide in transgenic mice renewed the search for the GRE. Analysis of a series of deletion constructs from this 17-kb region in cultured cells identified a single 455-bp region that conferred DEX induction on a reporter gene. This 455-bp region contains two GREs that bind to the glucocorticoid receptor as assessed by gel mobility shift. Deletion of this fragment from the 17-kb flanking region eliminates the DEX responsiveness of reporter genes. The two GREs, which are located ≈1 kb upstream of the MT-II gene and ≈7 kb upstream of the MT-I gene, are necessary for induction of both genes and can function independently of elements within the proximal promoter region of either gene.

Structural distribution of stability in a thermophilic enzyme

Stability parameters for individual residues in Thermus thermophilus cysteine-free RNase H were determined by native state hydrogen exchange, thus providing a unique comparison of regional thermodynamics between thermophilic and mesophilic homologues. The general distribution of stability in the thermophilic protein is similar to that of its mesophilic homologue, with a proportional increase in stability for almost all residues. As a consequence, the residue-specific stabilities of the two proteins are remarkably similar under conditions where their global stabilities are the same. These results indicate that T. thermophilus RNase H is stabilized in a delocalized fashion, preserving a finely tuned balance of stabilizing interactions throughout the structure. Therefore, although protein stability can be altered by single amino acid substitution, evolution for optimal function may require more subtle and delocalized mechanisms.

Cannabinoid CB1 receptors and ligands in vertebrate retina: Localization and function of an endogenous signaling system

CB1, a cannabinoid receptor enriched in neuronal tissue, was found in high concentration in retinas of rhesus monkey, mouse, rat, chick, goldfish, and tiger salamander by using a subtype-specific polyclonal antibody. Immunolabeling was detected in the two synaptic layers of the retina, the inner and outer plexiform layers, of all six species examined. In the outer plexiform layer, CB1 was located in and/or on cone pedicles and rod spherules. Labeling was detected in some amacrine cells of all species and in the ganglion cells and ganglion cell axons of all species except fish. In addition, sparse labeling was found in the inner and/or outer segments of the photoreceptors of monkey, mouse, rat, and chick. Using GC/MS to detect possible endogenous cannabinoids, we found 3 nmol of 2-arachidonylglycerol per g of tissue, but no anandamide was detectable. Cannabinoid receptor agonists induced a dramatic reduction in the amplitude of voltage-gated L-type calcium channel currents in identified retinal bipolar cells. The presence and distribution of the CB1 receptor, the large amounts of 2-arachidonylglycerol found, and the effects of cannabinoids on calcium channel activity in bipolar cells suggest a substantive role for an endogenous cannabinoid signaling system in retinal physiology, and perhaps vision in general.

Structure and function in rhodopsin: Rhodopsin mutants with a neutral amino acid at E134 have a partially activated conformation in the dark state*

The Glu-134–Arg-135 residues in rhodopsin, located near the cytoplasmic end of the C helix, are involved in G protein binding, or activation, or both. Furthermore, the charge-neutralizing mutation Glu-134 to Gln-134 produces hyperactivity in the activated state and produces constitutive activity in opsin. The Glu/Asp-Arg charge pair is highly conserved in equivalent positions in other G protein-coupled receptors. To investigate the structural consequences of charge-neutralizing mutations at Glu-134 and Arg-135 in rhodopsin, single spin-labeled side chains were introduced at sites in the cytoplasmic domains of helices C (140), E (227), F (250), or G (316) to serve as “molecular sensors” of the local helix bundle conformation. In each of the spin-labeled rhodopsins, a Gln substitution was introduced at either Glu-134 or Arg-135, and the electron paramagnetic resonance spectrum of the spin label was used to monitor the structural response of the helix bundle. The results indicate that a Gln substitution at Glu-134 induces a photoactivated conformation around helices C and G even in the dark state, an observation of potential relevance to the hyperactivity and constitutive activity of the mutant. In contrast, little change is induced in helix F, which has been shown to undergo a dominant motion upon photoactivation. This result implies that the multiple helix motions accompanying photoactivation are not strongly coupled and can be induced to take place independently. Gln substitution at Arg-135 produces only minor structural changes in the dark- or light-activated conformation, suggesting that this residue is not a determinant of structure in the regions investigated, although it may be functionally important.

Heterogeneous Distribution of the Unusual Phospholipid Semilysobisphosphatidic Acid through the Golgi Complex

To investigate the distribution of lipids through the Golgi complex, we analyzed the envelopes of several viruses that assemble in different subcompartments of the Golgi, as well as subcellular fractions. Our results indicate that each Golgi subcompartment has a distinct phospholipid composition due mainly to differences in the relative amounts of semilysobisphosphatidic acid (SLBPA), sphingomyelin, phosphatidylserine, and phosphatidylinositol. Interestingly, SLBPA is enriched in the adjacent Golgi networks compared with the Golgi stack, and this enrichment varies with cell type. The heterogeneous distribution of SLBPA through the Golgi complex suggests it may play an important role in the structure and/or function of this organelle.

A Mutant of Arp2p Causes Partial Disassembly of the Arp2/3 Complex and Loss of Cortical Actin Function in Fission Yeast

The Arp2/3 complex is an essential component of the yeast actin cytoskeleton that localizes to cortical actin patches. We have isolated and characterized a temperature-sensitive mutant of Schizosaccharomyces pombe arp2 that displays a defect in cortical actin patch distribution. The arp2+ gene encodes an essential actin-related protein that colocalizes with actin at the cortical actin patch. Sucrose gradient analysis of the Arp2/3 complex in the arp2-1 mutant indicated that the Arp2p and Arc18p subunits are specifically lost from the complex at restrictive temperature. These results are consistent with immunolocalization studies of the mutant that show that Arp2-1p is diffusely localized in the cytoplasm at restrictive temperature. Interestingly, Arp3p remains localized to the cortical actin patch under the same restrictive conditions, leading to the hypothesis that loss of Arp2p from the actin patch affects patch motility but does not severely compromise its architecture. Analysis of the mutant Arp2 protein demonstrated defects in ATP and Arp3p binding, suggesting a possible model for disruption of the complex.

The Dynamin-like Protein DLP1 Is Essential for Normal Distribution and Morphology of the Endoplasmic Reticulum and Mitochondria in Mammalian Cells

The dynamin family of large GTPases has been implicated in vesicle formation from both the plasma membrane and various intracellular membrane compartments. The dynamin-like protein DLP1, recently identified in mammalian tissues, has been shown to be more closely related to the yeast dynamin proteins Vps1p and Dnm1p (42%) than to the mammalian dynamins (37%). Furthermore, DLP1 has been shown to associate with punctate vesicles that are in intimate contact with microtubules and the endoplasmic reticulum (ER) in mammalian cells. To define the function of DLP1, we have transiently expressed both wild-type and two mutant DLP1 proteins, tagged with green fluorescent protein, in cultured mammalian cells. Point mutations in the GTP-binding domain of DLP1 (K38A and D231N) dramatically changed its intracellular distribution from punctate vesicular structures to either an aggregated or a diffuse pattern. Strikingly, cells expressing DLP1 mutants or microinjected with DLP1 antibodies showed a marked reduction in ER fluorescence and a significant aggregation and tubulation of mitochondria by immunofluorescence microscopy. Consistent with these observations, electron microscopy of DLP1 mutant cells revealed a striking and quantitative change in the distribution and morphology of mitochondria and the ER. These data support very recent studies by other authors implicating DLP1 in the maintenance of mitochondrial morphology in both yeast and mammalian cells. Furthermore, this study provides the first evidence that a dynamin family member participates in the maintenance and distribution of the ER. How DLP1 might participate in the biogenesis of two presumably distinct organelle systems is discussed.

Agrin in Alzheimer’s disease: Altered solubility and abnormal distribution within microvasculature and brain parenchyma

Agrin is a heparan sulfate proteoglycan that is widely expressed in neurons and microvascular basal lamina in the rodent and avian central nervous system. Agrin induces the differentiation of nerve-muscle synapses, but its function in either normal or diseased brains is not known. Alzheimer’s disease (AD) is characterized by loss of synapses, changes in microvascular architecture, and formation of neurofibrillary tangles and senile plaques. Here we have asked whether AD causes changes in the distribution and biochemical properties of agrin. Immunostaining of normal, aged human central nervous system revealed that agrin is expressed in neurons in multiple brain areas. Robust agrin immunoreactivity was observed uniformly in the microvascular basal lamina. In AD brains, agrin is highly concentrated in both diffuse and neuritic plaques as well as neurofibrillary tangles; neuronal expression of agrin also was observed. Furthermore, patients with AD had microvascular alterations characterized by thinning and fragmentation of the basal lamina. Detergent extraction and Western blotting showed that virtually all the agrin in normal brain is soluble in 1% SDS. In contrast, a large fraction of the agrin in AD brains is insoluble under these conditions, suggesting that it is tightly associated with β-amyloid. Together, these data indicate that the agrin abnormalities observed in AD are closely linked to β-amyloid deposition. These observations suggest that altered agrin expression in the microvasculature and the brain parenchyma contribute to the pathogenesis of AD.

Controlling small guanine–nucleotide-exchange factor function through cytoplasmic RNA intramers

ADP-ribosylation factor (ARF) GTPases and their regulatory proteins have been implicated in the control of diverse biological functions. Two main classes of positive regulatory elements for ARF have been discovered so far: the large Sec7/Gea and the small cytohesin/ARNO families, respectively. These proteins harbor guanine–nucleotide-exchange factor (GEF) activity exerted by the common Sec7 domain. The availability of a specific inhibitor, the fungal metabolite brefeldin A, has enabled documentation of the involvement of the large GEFs in vesicle transport. However, because of the lack of such tools, the biological roles of the small GEFs have remained controversial. Here, we have selected a series of RNA aptamers that specifically recognize the Sec7 domain of cytohesin 1. Some aptamers inhibit guanine–nucleotide exchange on ARF1, thereby preventing ARF activation in vitro. Among them, aptamer M69 exhibited unexpected specificity for the small GEFs, because it does not interact with or inhibit the GEF activity of the related Gea2-Sec7 domain, a member of the class of large GEFs. The inhibitory effect demonstrated in vitro clearly is observed as well in vivo, based on the finding that M69 produces similar results as a dominant-negative, GEF-deficient mutant of cytohesin 1: when expressed in the cytoplasm of T-cells, M69 reduces stimulated adhesion to intercellular adhesion molecule-1 and results in a dramatic reorganization of F-actin distribution. These highly specific cellular effects suggest that the ARF-GEF activity of cytohesin 1 plays an important role in cytoskeletal remodeling events of lymphoid cells.

In vivo restoration of laminin 5 β3 expression and function in junctional epidermolysis bullosa

The blistering disorder, lethal junctional epidermolysis bullosa (JEB), can result from mutations in the LAMB3 gene, which encodes laminin 5 β3 (β3). Appropriate expression of LAMβ3 in JEB skin tissue could potentially ameliorate the symptoms of the underlying disease. To explore the utility of this therapeutic approach, primary keratinocytes from six unrelated JEB patients were transduced with a retroviral vector encoding β3 and used to regenerate human skin on severe combined immunodeficient (SCID) mice. Tissue regenerated from β3-transduced JEB keratinocytes produced phenotypically normal skin characterized by sustained β3 expression and the formation of hemidesmosomes. Additionally, β3 gene transfer corrected the distribution of a number of important basement membrane zone proteins including BPAG2, integrins β4/β1, and laminins α3/γ2. Skin produced from β3-negative (β3[−]) JEB cells mimicked the hallmarks of the disease state and did not exhibit any of the aforementioned traits. Therefore, by effecting therapeutic gene transfer to β3-deficient primary keratinocytes, it is possible to produce healthy, normal skin tissue in vivo. These data support the utility of gene therapy for JEB and highlight the potential for gene delivery in the treatment of human genetic skin disease.