Interactions between roughness and topography in hydraulic models

Analysis of river flow using hydraulic modelling and its implications in derived environ-mental applications are inextricably connected with the way in which the river boundary shape is represented. This relationship is scale-dependent upon the modelling resolution which in turn determines the importance of a subscale performance of the model and the way subscale (surface and flow) processes are parameterised. Commonly, the subscale behaviour of the model relies upon a roughness parameterisation whose meaning depends on the dimensionality of the hydraulic model and the resolution of the topographic represen¬tation scale. This latter is, in turn, dependent on the resolution of the computational mesh as well as on the detail of measured topographic data. Flow results are affected by this interactions between scale and subscale parameterisation according to the dimensionality approach. The aim of this dissertation is the evaluation of these interactions upon hy¬draulic modelling results. Current high resolution topographic source availability induce this research which is tackled using a suitable roughness approach according to each di¬mensionality with the purpose of the interaction assessment. A 1D HEC-RAS model, a 2D raster-based diffusion-wave model with a scale-dependent distributed roughness parame-terisation and a 3D finite volume scheme with a porosity algorithm approach to incorporate complex topography have been used. Different topographic sources are assessed using a 1D scheme. LiDAR data are used to isolate the mesh resolution from the topographic content of the DEM effects upon 2D and 3D flow results. A distributed roughness parameterisation, using a roughness height approach dependent upon both mesh resolution and topographic content is developed and evaluated for the 2D scheme. Grain-size data and fractal methods are used for the reconstruction of topography with microscale information, required for some applications but not easily available. Sensitivity of hydraulic parameters to this topographic parameterisation is evaluated in a 3D scheme at different mesh resolu¬tions. Finally, the structural variability of simulated flow is analysed and related to scale interactions. Model simulations demonstrate (i) the importance of the topographic source in a 1D models; (ii) the mesh resolution approach is dominant in 2D and 3D simulations whereas in a 1D model the topographic source and even the roughness parameterisation impacts are more critical; (iii) the increment of the sensitivity to roughness parameterisa-tion in 1D and 2D schemes with detailed topographic sources and finer mesh resolutions; and (iv) the topographic content and microtopography impact throughout the vertical profile of computed 3D velocity in a depth-dependent way, whereas 2D results are not affected by topographic content variations. Finally, the spatial analysis shows that the mesh resolution controls high resolution model scale results, roughness parameterisation control 2D simulation results for a constant mesh resolution; and topographic content and micro-topography variations impacts upon the organisation of flow results depth-dependently in a 3D scheme. Resumen La topografía juega un papel fundamental en la distribución del agua y la energía en los paisajes naturales (Beven and Kirkby 1979; Wood et al. 1997). La simulación hidráulica combinada con métodos de medición del terreno por teledetección constituyen una poderosa herramienta de investigación en la comprensión del comportamiento de los flujos de agua debido a la variabilidad de la superficie sobre la que fluye. La representación e incorporación de la topografía en el esquema hidráulico tiene una importancia crucial en los resultados y determinan el desarrollo de sus aplicaciones al campo medioambiental. Cualquier simulación es una simplificación de un proceso del mundo real, y por tanto el grado de simplificación determinará el significado de los resultados simulados. Este razonamiento es particularmente difícil de trasladar a la simulación hidráulica donde aspectos de la escala tan diferentes como la escala de los procesos de flujo y de representación del contorno son considerados conjuntamente incluso en fases de parametrización (e.g. parametrización de la rugosidad). Por una parte, esto es debido a que las decisiones de escala vienen condicionadas entre ellas (e.g. la dimensionalidad del modelo condiciona la escala de representación del contorno) y por tanto interaccionan en sus resultados estrechamente. Y por otra parte, debido a los altos requerimientos numéricos y computacionales de una representación explícita de alta resolución de los procesos de flujo y discretización de la malla. Además, previo a la modelización hidráulica, la superficie del terreno sobre la que el agua fluye debe ser modelizada y por tanto presenta su propia escala de representación, que a su vez dependerá de la escala de los datos topográficos medidos con que se elabora el modelo. En última instancia, esta topografía es la que determina el comportamiento espacial del flujo. Por tanto, la escala de la topografía en sus fases de medición y modelización (resolución de los datos y representación topográfica) previas a su incorporación en el modelo hidráulico producirá a su vez un impacto que se acumulará al impacto global resultante debido a la escala computacional del modelo hidráulico y su dimensión. La comprensión de las interacciones entre las complejas geometrías del contorno y la estructura del flujo utilizando la modelización hidráulica depende de las escalas consideradas en la simplificación de los procesos hidráulicos y del terreno (dimensión del modelo, tamaño de escala computacional y escala de los datos topográficos). La naturaleza de la aplicación del modelo hidráulico (e.g. habitat físico, análisis de riesgo de inundaciones, transporte de sedimentos) determina en primer lugar la escala del estudio y por tanto el detalle de los procesos a simular en el modelo (i.e. la dimensionalidad) y, en consecuencia, la escala computacional a la que se realizarán los cálculos (i.e. resolución computacional). Esta última a su vez determina, el detalle geográfico con que deberá representarse el contorno acorde con la resolución de la malla computacional. La parametrización persigue incorporar en el modelo hidráulico la cuantificación de los procesos y condiciones físicas del sistema natural y por tanto debe incluir no solo aquellos procesos que tienen lugar a la escala de modelización, sino también aquellos que tienen lugar a un nivel subescalar y que deben ser definidos mediante relaciones de escalado con las variables modeladas explícitamente. Dicha parametrización se implementa en la práctica mediante la provisión de datos al modelo, por tanto la escala de los datos geográficos utilizados para parametrizar el modelo no sólo influirá en los resultados, sino también determinará la importancia del comportamiento subescalar del modelo y el modo en que estos procesos deban ser parametrizados (e.g. la variabilidad natural del terreno dentro de la celda de discretización o el flujo en las direcciones laterales y verticales en un modelo unidimensional). En esta tesis, se han utilizado el modelo unidimensional HEC-RAS, (HEC 1998b), un modelo ráster bidimensional de propagación de onda, (Yu 2005) y un esquema tridimensional de volúmenes finitos con un algoritmo de porosidad para incorporar la topografía, (Lane et al. 2004; Hardy et al. 2005). La geometría del contorno viene definida por la escala de representación topográfica (resolución de malla y contenido topográfico), la cual a su vez depende de la escala de la fuente cartográfica. Todos estos factores de escala interaccionan en la respuesta del modelo hidráulico a la topografía. En los últimos años, métodos como el análisis fractal y las técnicas geoestadísticas utilizadas para representar y analizar elementos geográficos (e.g. en la caracterización de superficies (Herzfeld and Overbeck 1999; Butler et al. 2001)), están promoviendo nuevos enfoques en la cuantificación de los efectos de escala (Lam et al. 2004; Atkinson and Tate 2000; Lam et al. 2006) por medio del análisis de la estructura espacial de la variable (e.g. Bishop et al. 2006; Ju et al. 2005; Myint et al. 2004; Weng 2002; Bian and Xie 2004; Southworth et al. 2006; Pozd-nyakova et al. 2005; Kyriakidis and Goodchild 2006). Estos métodos cuantifican tanto el rango de valores de la variable presentes a diferentes escalas como la homogeneidad o heterogeneidad de la variable espacialmente distribuida (Lam et al. 2004). En esta tesis, estas técnicas se han utilizado para analizar el impacto de la topografía sobre la estructura de los resultados hidráulicos simulados. Los datos de teledetección de alta resolución y técnicas GIS también están siendo utilizados para la mejor compresión de los efectos de escala en modelos medioambientales (Marceau 1999; Skidmore 2002; Goodchild 2003) y se utilizan en esta tesis. Esta tesis como corpus de investigación aborda las interacciones de esas escalas en la modelización hidráulica desde un punto de vista global e interrelacionado. Sin embargo, la estructura y el foco principal de los experimentos están relacionados con las nociones espaciales de la escala de representación en relación con una visión global de las interacciones entre escalas. En teoría, la representación topográfica debe caracterizar la superficie sobre la que corre el agua a una adecuada (conforme a la finalidad y dimensión del modelo) escala de discretización, de modo que refleje los procesos de interés. La parametrización de la rugosidad debe de reflejar los efectos de la variabilidad de la superficie a escalas de más detalle que aquellas representadas explícitamente en la malla topográfica (i.e. escala de discretización). Claramente, ambos conceptos están físicamente relacionados por un

Detecting unknown attacks in wireless sensor networks that contain mobile nodes

As wireless sensor networks are usually deployed in unattended areas, security policies cannot be updated in a timely fashion upon identification of new attacks. This gives enough time for attackers to cause significant damage. Thus, it is of great importance to provide protection from unknown attacks. However, existing solutions are mostly concentrated on known attacks. On the other hand, mobility can make the sensor network more resilient to failures, reactive to events, and able to support disparate missions with a common set of sensors, yet the problem of security becomes more complicated. In order to address the issue of security in networks with mobile nodes, we propose a machine learning solution for anomaly detection along with the feature extraction process that tries to detect temporal and spatial inconsistencies in the sequences of sensed values and the routing paths used to forward these values to the base station. We also propose a special way to treat mobile nodes, which is the main novelty of this work. The data produced in the presence of an attacker are treated as outliers, and detected using clustering techniques. These techniques are further coupled with a reputation system, in this way isolating compromised nodes in timely fashion. The proposal exhibits good performances at detecting and confining previously unseen attacks, including the cases when mobile nodes are compromised.

Spatial effects on rural commerce

Commerce in rural territories should not be considered as a needed service, but as a basic infrastructure, that impact not only existent population, but also tourism, and rural industrialization. So, the rural areas need not only agriculture but industry and services, to have a global and balanced development, including for the countryside and the population. In the work presented in this paper, we are considering the formulation of the direct relation between population and the endowment of commerce sites within a geographical territory, the ?area of commercial interactions?. These are the closer set of towns that can gravitate to each other to cover the required needs for the populations within the area. The products retailed, range from basic products for the daily lives, to all other products for industry, agriculture, and services. The econometric spatial model developed to evaluate the interactions and estimate the parameters, is based on the Spatial Error Model, which allows for other spatial hidden effects to be considered without direct interference to the commercial disposition. The data and territory used to test the model correspond to a rural area in the Spanish Palencia territory (NUTS-3 level). The parameters have dependence from population levels, local rent per head, local and regional government budgets, and particular spatial restrictions. Interesting results are emerging form the model. The more significant is that the spatial effects can replace some number of commerce sites in towns, given the right spatial distribution of the sites and the towns. This is equivalent to consider the area of commercial interactions as the unit of measurement for the basic infrastructure and not only the towns.

An attitude-based reasoning strategy to enhance interaction with augmented objects

This paper describes a mobile-based system to interact with objects in smart spaces, where the offer of resources may be extensive. The underlying idea is to use the augmentation capabilities of the mobile device to enable it as user-object mediator. In particular, the paper details how to build an attitude-based reasoning strategy that facilitates user-object interaction and resource filtering. The strategy prioritizes the available resources depending on the spatial history of the user, his real-time location and orientation and, finally, his active touch and focus interactions with the virtual overlay. The proposed reasoning method has been partially validated through a prototype that handles 2D and 3D visualization interfaces. This framework makes possible to develop in practice the IoT paradigm, augmenting the objects without physically modifying them.

Assessment of "mobile mapping system": A GIS-based support methodology

In this article, the authors examine the current status of different elements that integrate the landscape of the municipality of Olias del Rey in Toledo (Spain). A methodology for the study of rural roads, activity farming and local hunting management. We used Geographic Information Technologies (GIT) in order to optimize spatial information including the design of a Geographic Information System (GIS). In the acquisition of field data we have used vehicle "mobile mapping" instrumentation equipped with GNSS, LiDAR, digital cameras and odometer. The main objective is the integration of geoinformation and geovisualization of the information to provide a fundamental tool for rural planning and management.

Spatial sampling methods for improved communication for wireless relay robots

Having reliable wireless communication in a network of mobile robots is an ongoing challenge, especially when the mobile robots are given tasks in hostile or harmful environments such as radiation environments in scientific facilities, tunnels with large metallic components and complicated geometries as found at CERN. In this paper, we propose a decentralised method for improving the wireless network throughput by optimizing the wireless relay robot position to receive the best wireless signal strength using implicit spatial diversity concepts and gradient-search algorithms. We experimentally demonstrate the effectiveness of the proposed solutions with a KUKA Youbot omni-directional mobile robot. The performance of the algorithms is compared under various scenarios in an underground scientific facility at CERN.

Wireless communication enhancement methods for mobile robots in radiation environments

En entornos hostiles tales como aquellas instalaciones científicas donde la radiación ionizante es el principal peligro, el hecho de reducir las intervenciones humanas mediante el incremento de las operaciones robotizadas está siendo cada vez más de especial interés. CERN, la Organización Europea para la Investigación Nuclear, tiene alrededor de unos 50 km de superficie subterránea donde robots móviles controlador de forma remota podrían ayudar en su funcionamiento, por ejemplo, a la hora de llevar a cabo inspecciones remotas sobre radiación en los diferentes áreas destinados al efecto. No solo es preciso considerar que los robots deben ser capaces de recorrer largas distancias y operar durante largos periodos de tiempo, sino que deben saber desenvolverse en los correspondientes túneles subterráneos, tener en cuenta la presencia de campos electromagnéticos, radiación ionizante, etc. y finalmente, el hecho de que los robots no deben interrumpir el funcionamiento de los aceleradores. El hecho de disponer de un sistema de comunicaciones inalámbrico fiable y robusto es esencial para la correcta ejecución de las misiones que los robots deben afrontar y por supuesto, para evitar tales situaciones en las que es necesario la recuperación manual de los robots al agotarse su energía o al perder el enlace de comunicaciones. El objetivo de esta Tesis es proveer de las directrices y los medios necesarios para reducir el riesgo de fallo en la misión y maximizar las capacidades de los robots móviles inalámbricos los cuales disponen de almacenamiento finito de energía al trabajar en entornos peligrosos donde no se dispone de línea de vista directa. Para ello se proponen y muestran diferentes estrategias y métodos de comunicación inalámbrica. Teniendo esto en cuenta, se presentan a continuación los objetivos de investigación a seguir a lo largo de la Tesis: predecir la cobertura de comunicaciones antes y durante las misiones robotizadas; optimizar la capacidad de red inalámbrica de los robots móviles con respecto a su posición; y mejorar el rango operacional de esta clase de robots. Por su parte, las contribuciones a la Tesis se citan más abajo. El primer conjunto de contribuciones son métodos novedosos para predecir el consumo de energía y la autonomía en la comunicación antes y después de disponer de los robots en el entorno seleccionado. Esto es importante para proporcionar conciencia de la situación del robot y evitar fallos en la misión. El consumo de energía se predice usando una estrategia propuesta la cual usa modelos de consumo provenientes de diferentes componentes en un robot. La predicción para la cobertura de comunicaciones se desarrolla usando un nuevo filtro de RSS (Radio Signal Strength) y técnicas de estimación con la ayuda de Filtros de Kalman. El segundo conjunto de contribuciones son métodos para optimizar el rango de comunicaciones usando novedosas técnicas basadas en muestreo espacial que son robustas frente a ruidos de campos de detección y radio y que proporcionan redundancia. Se emplean métodos de diferencia central finitos para determinar los gradientes 2D RSS y se usa la movilidad del robot para optimizar el rango de comunicaciones y la capacidad de red. Este método también se valida con un caso de estudio centrado en la teleoperación háptica de robots móviles inalámbricos. La tercera contribución es un algoritmo robusto y estocástico descentralizado para la optimización de la posición al considerar múltiples robots autónomos usados principalmente para extender el rango de comunicaciones desde la estación de control al robot que está desarrollando la tarea. Todos los métodos y algoritmos propuestos se verifican y validan usando simulaciones y experimentos de campo con variedad de robots móviles disponibles en CERN. En resumen, esta Tesis ofrece métodos novedosos y demuestra su uso para: predecir RSS; optimizar la posición del robot; extender el rango de las comunicaciones inalámbricas; y mejorar las capacidades de red de los robots móviles inalámbricos para su uso en aplicaciones dentro de entornos peligrosos, que como ya se mencionó anteriormente, se destacan las instalaciones científicas con emisión de radiación ionizante. En otros términos, se ha desarrollado un conjunto de herramientas para mejorar, facilitar y hacer más seguras las misiones de los robots en entornos hostiles. Esta Tesis demuestra tanto en teoría como en práctica que los robots móviles pueden mejorar la calidad de las comunicaciones inalámbricas mediante la profundización en el estudio de su movilidad para optimizar dinámicamente sus posiciones y mantener conectividad incluso cuando no existe línea de vista. Los métodos desarrollados en la Tesis son especialmente adecuados para su fácil integración en robots móviles y pueden ser aplicados directamente en la capa de aplicación de la red inalámbrica. ABSTRACT In hostile environments such as in scientific facilities where ionising radiation is a dominant hazard, reducing human interventions by increasing robotic operations are desirable. CERN, the European Organization for Nuclear Research, has around 50 km of underground scientific facilities, where wireless mobile robots could help in the operation of the accelerator complex, e.g. in conducting remote inspections and radiation surveys in different areas. The main challenges to be considered here are not only that the robots should be able to go over long distances and operate for relatively long periods, but also the underground tunnel environment, the possible presence of electromagnetic fields, radiation effects, and the fact that the robots shall in no way interrupt the operation of the accelerators. Having a reliable and robust wireless communication system is essential for successful execution of such robotic missions and to avoid situations of manual recovery of the robots in the event that the robot runs out of energy or when the robot loses its communication link. The goal of this thesis is to provide means to reduce risk of mission failure and maximise mission capabilities of wireless mobile robots with finite energy storage capacity working in a radiation environment with non-line-of-sight (NLOS) communications by employing enhanced wireless communication methods. Towards this goal, the following research objectives are addressed in this thesis: predict the communication range before and during robotic missions; optimise and enhance wireless communication qualities of mobile robots by using robot mobility and employing multi-robot network. This thesis provides introductory information on the infrastructures where mobile robots will need to operate, the tasks to be carried out by mobile robots and the problems encountered in these environments. The reporting of research work carried out to improve wireless communication comprises an introduction to the relevant radio signal propagation theory and technology followed by explanation of the research in the following stages: An analysis of the wireless communication requirements for mobile robot for different tasks in a selection of CERN facilities; predictions of energy and communication autonomies (in terms of distance and time) to reduce risk of energy and communication related failures during missions; autonomous navigation of a mobile robot to find zone(s) of maximum radio signal strength to improve communication coverage area; and autonomous navigation of one or more mobile robots acting as mobile wireless relay (repeater) points in order to provide a tethered wireless connection to a teleoperated mobile robot carrying out inspection or radiation monitoring activities in a challenging radio environment. The specific contributions of this thesis are outlined below. The first sets of contributions are novel methods for predicting the energy autonomy and communication range(s) before and after deployment of the mobile robots in the intended environments. This is important in order to provide situational awareness and avoid mission failures. The energy consumption is predicted by using power consumption models of different components in a mobile robot. This energy prediction model will pave the way for choosing energy-efficient wireless communication strategies. The communication range prediction is performed using radio signal propagation models and applies radio signal strength (RSS) filtering and estimation techniques with the help of Kalman filters and Gaussian process models. The second set of contributions are methods to optimise the wireless communication qualities by using novel spatial sampling based techniques that are robust to sensing and radio field noises and provide redundancy features. Central finite difference (CFD) methods are employed to determine the 2-D RSS gradients and use robot mobility to optimise the communication quality and the network throughput. This method is also validated with a case study application involving superior haptic teleoperation of wireless mobile robots where an operator from a remote location can smoothly navigate a mobile robot in an environment with low-wireless signals. The third contribution is a robust stochastic position optimisation algorithm for multiple autonomous relay robots which are used for wireless tethering of radio signals and thereby to enhance the wireless communication qualities. All the proposed methods and algorithms are verified and validated using simulations and field experiments with a variety of mobile robots available at CERN. In summary, this thesis offers novel methods and demonstrates their use to predict energy autonomy and wireless communication range, optimise robots position to improve communication quality and enhance communication range and wireless network qualities of mobile robots for use in applications in hostile environmental characteristics such as scientific facilities emitting ionising radiations. In simpler terms, a set of tools are developed in this thesis for improving, easing and making safer robotic missions in hostile environments. This thesis validates both in theory and experiments that mobile robots can improve wireless communication quality by exploiting robots mobility to dynamically optimise their positions and maintain connectivity even when the (radio signal) environment possess non-line-of-sight characteristics. The methods developed in this thesis are well-suited for easier integration in mobile robots and can be applied directly at the application layer of the wireless network. The results of the proposed methods have outperformed other comparable state-of-the-art methods.

Multisensor data fusion for accurate modelling of mobile objects

In the last decade, multi-sensor data fusion has become a broadly demanded discipline to achieve advanced solutions that can be applied in many real world situations, either civil or military. In Defence,accurate detection of all target objects is fundamental to maintaining situational awareness, to locating threats in the battlefield and to identifying and protecting strategically own forces. Civil applications, such as traffic monitoring, have similar requirements in terms of object detection and reliable identification of incidents in order to ensure safety of road users. Thanks to the appropriate data fusion technique, we can give these systems the power to exploit automatically all relevant information from multiple sources to face for instance mission needs or assess daily supervision operations. This paper focuses on its application to active vehicle monitoring in a particular area of high density traffic, and how it is redirecting the research activities being carried out in the computer vision, signal processing and machine learning fields for improving the effectiveness of detection and tracking in ground surveillance scenarios in general. Specifically, our system proposes fusion of data at a feature level which is extracted from a video camera and a laser scanner. In addition, a stochastic-based tracking which introduces some particle filters into the model to deal with uncertainty due to occlusions and improve the previous detection output is presented in this paper. It has been shown that this computer vision tracker contributes to detect objects even under poor visual information. Finally, in the same way that humans are able to analyze both temporal and spatial relations among items in the scene to associate them a meaning, once the targets objects have been correctly detected and tracked, it is desired that machines can provide a trustworthy description of what is happening in the scene under surveillance. Accomplishing so ambitious task requires a machine learning-based hierarchic architecture able to extract and analyse behaviours at different abstraction levels. A real experimental testbed has been implemented for the evaluation of the proposed modular system. Such scenario is a closed circuit where real traffic situations can be simulated. First results have shown the strength of the proposed system.

Changes in spatial point patterns of pioneer woody plants across a large tropical landslide

We assessed whether the relative importance of positive and negative interactions in early successional communities varied across a large landslide on Casita Volcano (Nicaragua). We tested several hypotheses concerning the signatures of these processes in the spatial patterns of woody pioneer plants, as well as those of mortality and recruitment events, in several zones of the landslide differing in substrate stability and fertility, over a period of two years (2001 and 2002). We identified all woody individuals with a diameter >1 cm and mapped them in 28 plots measuring 10 × 10-m. On these maps, we performed a spatial point pattern analysis using univariate and bivariate pair-correlation functions; g (r) and g12 (r), and pairwise differences of univariate and bivariate functions. Spatial signatures of positive and negative interactions among woody plants were more prevalent in the most and least stressful zones of the landslide, respectively. Natural and human-induced disturbances such as the occurrence of fire, removal of newly colonizing plants through erosion and clearcutting of pioneer trees were also identified as potentially important pattern-creating processes. These results are in agreement with the stress-gradient hypothesis, which states that the relative importance of facilitation and competition varies inversely across gradients of abiotic stress. Our findings also indicate that the assembly of early successional plant communities in large heterogeneous landslides might be driven by a much larger array of processes than previously thought.

Fe-catalyzed cleavage of the α subunit of Na/K-ATPase: Evidence for conformation-sensitive interactions between cytoplasmic domains

Incubation of Na/K-ATPase with ascorbate plus H2O2 produces specific cleavage of the α subunit. Five fragments with intact C termini and complementary fragments with intact N termini were observed. The β subunit is not cleaved. Cleavages depend on the presence of contaminant or added Fe2+ ions, as inferred by suppression of cleavages with nonspecific metal complexants (histidine, EDTA, phenanthroline) or the Fe3+-specific complexant desferrioxamine, or acceleration of cleavages by addition of low concentrations of Fe2+ but not of other heavy metal ions. Na/K-ATPase is inactivated in addition to cleavage, and both effects are insensitive to OH⋅ radical scavengers. Cleavages are sensitive to conformation. In low ionic strength media (E2) or media containing Rb ions [E2(Rb)], cleavage is much faster than in high ionic strength media (E1) or media containing Na ions (E1Na). N-terminal fragments and two C-terminal fragments (N-terminals E214 and V712) have been identified by amino acid sequencing. Approximate positions of other cleavages were determined with specific antibodies. The results suggest that Fe2+ (or Fe3+) ions bind with high affinity at the cytoplasmic surface and catalyze cleavages of peptide bonds close to the Fe2+ (or Fe3+) ion. Thus, cleavage patterns can provide information on spatial organization of the polypeptide chain. We propose that highly conserved regions of the α subunit, within the minor and major cytoplasmic loops, interact in the E2 or E2(Rb) conformations but move apart in the E1 or E1Na conformations. We discuss implications of domain interactions for the energy transduction mechanism. Fe-catalyzed cleavages may be applicable to other P-type pumps or membrane proteins.

A modular misexpression screen in Drosophila detecting tissue-specific phenotypes.

Genetic screens in Drosophila have lead to the discovery of many genes important for patterning and signal transduction in diverse organisms. Traditionally, the phenotypic effects of loss-of-function mutations are analyzed. As an alternative way to link genes and function, I have developed a versatile misexpression screen in Drosophila, the first such screen in higher eukaryotes. The screen identifies genes that, when over- or misexpressed in a pattern of interest, give a specific phenotype or modulate an existing mutant phenotype. It is based on Gal4 transactivation of a mobile enhancer and promoter that "targets" random endogenous genes for expression. The modular design of the screen allows directed expression in any temporal or spatial pattern. When activated in the developing eye, 4% of target inserts gave dominant phenotypes. One insertion was in the gene encoding Ras GTPase-activating protein; its overexpression phenotype was strongly enhanced by a mutation in Ras1. Thus, biologically relevant phenotypes and genetic interactions are identified using this method. The screen is a powerful new tool for developmental genetics; similar approaches can also be developed for other organisms.

Interplay of structure and disorder in cochaperonin mobile loops.

Protein-protein interactions typically are characterized by highly specific interfaces that mediate binding with precisely tuned affinities. Binding of the Escherichia coli cochaperonin GroES to chaperonin GroEL is mediated, at least in part, by a mobile polypeptide loop in GroES that becomes immobilized in the GroEL/GroES/nucleotide complex. The bacteriophage T4 cochaperonin Gp31 possesses a similar highly flexible polypeptide loop in a region of the protein that shows low, but significant, amino acid similarity with GroES and other cochaperonins. When bound to GroEL, a synthetic peptide representing the mobile loop of either GroES or Gp31 adopts a characteristic bulged hairpin conformation as determined by transferred nuclear Overhauser effects in NMR spectra. Thermodynamic considerations suggest that flexible disorder in the cochaperonin mobile loops moderates their affinity for GroEL to facilitate cycles of chaperonin-mediated protein folding.

Enzyme-mediated spatial segregation on individual polymeric support beads: application to generation and screening of encoded combinatorial libraries.

Proteolysis of short N alpha-protected peptide substrates bound to polyoxyethylene-polystyrene beads releases selectively free amino sites in the enzyme-accessible "surface" area. The substantial majority of functional sites in the "interior" of the polymeric support are not reached by the enzyme and remain uncleaved (protected). Subsequent synthesis with two classes of orthogonal protecting groups-N alpha-tert-butyloxycarbonyl (Boc) and N alpha-9-fluorenylmethyloxy-carbonyl (Fmoc)-allows generation of two structures on the same bead. The surface structure is available for receptor interactions, whereas the corresponding interior structure is used for coding. Coding structures are usually readily sequenceable peptides. This "shaving" methodology was illustrated by the preparation of a peptide-encoded model peptide combinatorial library containing 1.0 x 10(5) members at approximately 6-fold degeneracy. From this single library, good ligands were selected for three different receptors: anti-beta-endorphin anti-body, streptavidin, and thrombin, and the binding structures were deduced correctly by sequencing the coding peptides present on the same beads.

Spatial integration and cortical dynamics.

Cells in adult primary visual cortex are capable of integrating information over much larger portions of the visual field than was originally thought. Moreover, their receptive field properties can be altered by the context within which local features are presented and by changes in visual experience. The substrate for both spatial integration and cortical plasticity is likely to be found in a plexus of long-range horizontal connections, formed by cortical pyramidal cells, which link cells within each cortical area over distances of 6-8 mm. The relationship between horizontal connections and cortical functional architecture suggests a role in visual segmentation and spatial integration. The distribution of lateral interactions within striate cortex was visualized with optical recording, and their functional consequences were explored by using comparable stimuli in human psychophysical experiments and in recordings from alert monkeys. They may represent the substrate for perceptual phenomena such as illusory contours, surface fill-in, and contour saliency. The dynamic nature of receptive field properties and cortical architecture has been seen over time scales ranging from seconds to months. One can induce a remapping of the topography of visual cortex by making focal binocular retinal lesions. Shorter-term plasticity of cortical receptive fields was observed following brief periods of visual stimulation. The mechanisms involved entailed, for the short-term changes, altering the effectiveness of existing cortical connections, and for the long-term changes, sprouting of axon collaterals and synaptogenesis. The mutability of cortical function implies a continual process of calibration and normalization of the perception of visual attributes that is dependent on sensory experience throughout adulthood and might further represent the mechanism of perceptual learning.

Prenatal monocular enucleation induces a selective loss of low-spatial-frequency cortical responses to the remaining eye.

During early development, interactions between the two eyes are critical in the formation of eye-specific domains within the lateral geniculate nucleus and the visual cortex. When monocular enucleation is done early in prenatal life, it induces remarkable anatomical and functional reorganizations of the visual pathways. Behavioral data have shown a loss in sensitivity to low-spatial-frequency gratings in cats. To correlate the behavioral observations with a possible change in the analysis of contrast at the level of primary visual areas we recorded visual evoked potentials at the 17/18 border in two cats enucleated prenatally (gestational age at enucleation, 39-42 days), three neonatal, two control animals, and one animal with a surgical removal of Y-ganglion fibers. Our results show a strong attenuation in the amplitude of response at all contrast values for gratings of low spatial frequency in prenatally enucleated cats, whereas neonatally enucleated and control animals present responses of comparable amplitude. We conclude that the behavioral results reflect the reduced sensitivity for low frequencies of visual cortical neurons. In addition, we define a critical period for the development of the contrast-sensitivity function that seems to be limited to the prenatal gestation period. We suggest that the prenatal interruption of binocular interactions leads to a functional elimination of the Y-ganglion system.