New insights into small molecules inhibitors and protein-protein interactions of VirB8 : a critical conserved component of the type IV secretion system.

Les systèmes bactériens de sécrétion de type IV (T4SS) sont constitués d’un ensemble de 8 à 12 protéines conservées. Ces dernières sont utilisées lors de la translocation de protéines, la translocation de complexes ADN-protéines mais aussi pour le transport de ces derniers au travers de la membrane cellulaire. Les T4SS, en tant que facteurs de virulence pour beaucoup de pathogènes comme Brucella suis, sont donc d’excellents modèles cibles pour le développement de médicaments d’antivirulence. Ces médicaments, en privant le pathogène de son facteur essentiel de virulence : le T4SS, constituent une alternative ou encore une amélioration des traitements antibiotiques utilisés actuellement. VirB8, un facteur d’assemblage conservé dans le T4SS, forme des dimères qui sont importants pour la fonction des T4SS dans ces pathogènes. De par ses interactions multiples, VirB8 est un excellent modèle pour l’analyse des facteurs d’assemblage mais aussi en tant que cible de médicaments qui empêcheraient son interaction avec d’autres protéines et qui, in fine, désarmeraient les bactéries en les privant de leur fonctions essentielles de virulence. À ce jour, nous savons qu’il existe un équilibre monomère-dimère et un processus d’homodimerization de VirB8 dont l’importance est vitale pour la fonctionnement biologique des T4SSs. En se basant sur des essais quantitatifs d’interaction, nous avons identifié (i) des sites potentiels d’interaction avec d’autres protéines VirB du T4SS mais aussi (ii) isolé des petites molécules inhibitrices afin de tester la fonction protéique de VirB8. Afin de déterminer les acides aminés importants pour l’hétérodimérization de VirB8 avec VirB10, nous avons effectué des expériences de mutagenèse aléatoire, de phage display et d’arrimage moléculaire in silico. Ces expériences ont démontré l’importance de trois acides aminés localisés sur le feuillet β : R160, S162, T164 et I165. Ces derniers seraient importants pour l’association de VirB8 avec VirB10 étant donné que leur mutagenèse entraine une diminution de la formation du complexe VirB8-VirB10. L’objectif actuel de notre projet de recherche est de pouvoir mieux comprendre mais aussi d’évaluer le rôle de VirB8 dans l’assemblage du T4SS. Grace à un méthode de criblage adaptée à partir de la structure de VirB8, nous avons pu identifié une petite molécule inhibitrice BAR-068, qui aurait un rôle prometteur dans l’inhibition du T4SS. Nous avons utilisé la spectroscopie par fluorescence, l’essai à deux hybrides, le cross-linking et la cristallographie afin de déterminer le mécanisme d'interaction existant entre VirB8 et BAR-068. Ces travaux pourraient permettre de nombreuses avancées, notamment en termes de compréhension des mécanismes d’inhibition du T4SS. Notre objectif ultime est de pouvoir caractériser la séquence d’évènements essentiels à l’assemblage et au fonctionnement du T4SS. De manière globale, notre projet de recherche permettrait de révéler les grands principes d’assemblage des protéines membranaires, les processus de sécrétion de protéines chez les bactéries mais aussi de proposer une nouvelle stratégie lors du développement de drogues antimicrobiennes.

Genetic Programming meets Model-Driven Development

Genetic programming is known to provide good solutions for many problems like the evolution of network protocols and distributed algorithms. In such cases it is most likely a hardwired module of a design framework that assists the engineer to optimize specific aspects of the system to be developed. It provides its results in a fixed format through an internal interface. In this paper we show how the utility of genetic programming can be increased remarkably by isolating it as a component and integrating it into the model-driven software development process. Our genetic programming framework produces XMI-encoded UML models that can easily be loaded into widely available modeling tools which in turn posses code generation as well as additional analysis and test capabilities. We use the evolution of a distributed election algorithm as an example to illustrate how genetic programming can be combined with model-driven development. This example clearly illustrates the advantages of our approach – the generation of source code in different programming languages.

Comprehensive evaluation of the WaterGAP3 model across climatic, physiographic, and anthropogenic gradients

In den letzten Jahrzehnten haben sich makroskalige hydrologische Modelle als wichtige Werkzeuge etabliert um den Zustand der globalen erneuerbaren Süßwasserressourcen flächendeckend bewerten können. Sie werden heutzutage eingesetzt um eine große Bandbreite wissenschaftlicher Fragestellungen zu beantworten, insbesondere hinsichtlich der Auswirkungen anthropogener Einflüsse auf das natürliche Abflussregime oder der Auswirkungen des globalen Wandels und Klimawandels auf die Ressource Wasser. Diese Auswirkungen lassen sich durch verschiedenste wasserbezogene Kenngrößen abschätzen, wie z.B. erneuerbare (Grund-)Wasserressourcen, Hochwasserrisiko, Dürren, Wasserstress und Wasserknappheit. Die Weiterentwicklung makroskaliger hydrologischer Modelle wurde insbesondere durch stetig steigende Rechenkapazitäten begünstigt, aber auch durch die zunehmende Verfügbarkeit von Fernerkundungsdaten und abgeleiteten Datenprodukten, die genutzt werden können, um die Modelle anzutreiben und zu verbessern. Wie alle makro- bis globalskaligen Modellierungsansätze unterliegen makroskalige hydrologische Simulationen erheblichen Unsicherheiten, die (i) auf räumliche Eingabedatensätze, wie z.B. meteorologische Größen oder Landoberflächenparameter, und (ii) im Besonderen auf die (oftmals) vereinfachte Abbildung physikalischer Prozesse im Modell zurückzuführen sind. Angesichts dieser Unsicherheiten ist es unabdingbar, die tatsächliche Anwendbarkeit und Prognosefähigkeit der Modelle unter diversen klimatischen und physiographischen Bedingungen zu überprüfen. Bisher wurden die meisten Evaluierungsstudien jedoch lediglich in wenigen, großen Flusseinzugsgebieten durchgeführt oder fokussierten auf kontinentalen Wasserflüssen. Dies steht im Kontrast zu vielen Anwendungsstudien, deren Analysen und Aussagen auf simulierten Zustandsgrößen und Flüssen in deutlich feinerer räumlicher Auflösung (Gridzelle) basieren. Den Kern der Dissertation bildet eine umfangreiche Evaluierung der generellen Anwendbarkeit des globalen hydrologischen Modells WaterGAP3 für die Simulation von monatlichen Abflussregimen und Niedrig- und Hochwasserabflüssen auf Basis von mehr als 2400 Durchflussmessreihen für den Zeitraum 1958-2010. Die betrachteten Flusseinzugsgebiete repräsentieren ein breites Spektrum klimatischer und physiographischer Bedingungen, die Einzugsgebietsgröße reicht von 3000 bis zu mehreren Millionen Quadratkilometern. Die Modellevaluierung hat dabei zwei Zielsetzungen: Erstens soll die erzielte Modellgüte als Bezugswert dienen gegen den jegliche weiteren Modellverbesserungen verglichen werden können. Zweitens soll eine Methode zur diagnostischen Modellevaluierung entwickelt und getestet werden, die eindeutige Ansatzpunkte zur Modellverbesserung aufzeigen soll, falls die Modellgüte unzureichend ist. Hierzu werden komplementäre Modellgütemaße mit neun Gebietsparametern verknüpft, welche die klimatischen und physiographischen Bedingungen sowie den Grad anthropogener Beeinflussung in den einzelnen Einzugsgebieten quantifizieren. WaterGAP3 erzielt eine mittlere bis hohe Modellgüte für die Simulation von sowohl monatlichen Abflussregimen als auch Niedrig- und Hochwasserabflüssen, jedoch sind für alle betrachteten Modellgütemaße deutliche räumliche Muster erkennbar. Von den neun betrachteten Gebietseigenschaften weisen insbesondere der Ariditätsgrad und die mittlere Gebietsneigung einen starken Einfluss auf die Modellgüte auf. Das Modell tendiert zur Überschätzung des jährlichen Abflussvolumens mit steigender Aridität. Dieses Verhalten ist charakteristisch für makroskalige hydrologische Modelle und ist auf die unzureichende Abbildung von Prozessen der Abflussbildung und –konzentration in wasserlimitierten Gebieten zurückzuführen. In steilen Einzugsgebieten wird eine geringe Modellgüte hinsichtlich der Abbildung von monatlicher Abflussvariabilität und zeitlicher Dynamik festgestellt, die sich auch in der Güte der Niedrig- und Hochwassersimulation widerspiegelt. Diese Beobachtung weist auf notwendige Modellverbesserungen in Bezug auf (i) die Aufteilung des Gesamtabflusses in schnelle und verzögerte Abflusskomponente und (ii) die Berechnung der Fließgeschwindigkeit im Gerinne hin. Die im Rahmen der Dissertation entwickelte Methode zur diagnostischen Modellevaluierung durch Verknüpfung von komplementären Modellgütemaßen und Einzugsgebietseigenschaften wurde exemplarisch am Beispiel des WaterGAP3 Modells erprobt. Die Methode hat sich als effizientes Werkzeug erwiesen, um räumliche Muster in der Modellgüte zu erklären und Defizite in der Modellstruktur zu identifizieren. Die entwickelte Methode ist generell für jedes hydrologische Modell anwendbar. Sie ist jedoch insbesondere für makroskalige Modelle und multi-basin Studien relevant, da sie das Fehlen von feldspezifischen Kenntnissen und gezielten Messkampagnen, auf die üblicherweise in der Einzugsgebietsmodellierung zurückgegriffen wird, teilweise ausgleichen kann.

ACTORS: A Model of Concurrent Computation in Distributed Systems

A foundational model of concurrency is developed in this thesis. We examine issues in the design of parallel systems and show why the actor model is suitable for exploiting large-scale parallelism. Concurrency in actors is constrained only by the availability of hardware resources and by the logical dependence inherent in the computation. Unlike dataflow and functional programming, however, actors are dynamically reconfigurable and can model shared resources with changing local state. Concurrency is spawned in actors using asynchronous message-passing, pipelining, and the dynamic creation of actors. This thesis deals with some central issues in distributed computing. Specifically, problems of divergence and deadlock are addressed. For example, actors permit dynamic deadlock detection and removal. The problem of divergence is contained because independent transactions can execute concurrently and potentially infinite processes are nevertheless available for interaction.

Hierarchical Object Recognition Using Libraries of Parameterized Model Sub-Parts

This thesis describes the development of a model-based vision system that exploits hierarchies of both object structure and object scale. The focus of the research is to use these hierarchies to achieve robust recognition based on effective organization and indexing schemes for model libraries. The goal of the system is to recognize parameterized instances of non-rigid model objects contained in a large knowledge base despite the presence of noise and occlusion. Robustness is achieved by developing a system that can recognize viewed objects that are scaled or mirror-image instances of the known models or that contain components sub-parts with different relative scaling, rotation, or translation than in models. The approach taken in this thesis is to develop an object shape representation that incorporates a component sub-part hierarchy- to allow for efficient and correct indexing into an automatically generated model library as well as for relative parameterization among sub-parts, and a scale hierarchy- to allow for a general to specific recognition procedure. After analysis of the issues and inherent tradeoffs in the recognition process, a system is implemented using a representation based on significant contour curvature changes and a recognition engine based on geometric constraints of feature properties. Examples of the system's performance are given, followed by an analysis of the results. In conclusion, the system's benefits and limitations are presented.

Structural Dynamics Model of a Cartesian Robot

Methods are developed for predicting vibration response characteristics of systems which change configuration during operation. A cartesian robot, an example of such a position-dependent system, served as a test case for these methods and was studied in detail. The chosen system model was formulated using the technique of Component Mode Synthesis (CMS). The model assumes that he system is slowly varying, and connects the carriages to each other and to the robot structure at the slowly varying connection points. The modal data required for each component is obtained experimentally in order to get a realistic model. The analysis results in prediction of vibrations that are produced by the inertia forces as well as gravity and friction forces which arise when the robot carriages move with some prescribed motion. Computer simulations and experimental determinations are conducted in order to calculate the vibrations at the robot end-effector. Comparisons are shown to validate the model in two ways: for fixed configuration the mode shapes and natural frequencies are examined, and then for changing configuration the residual vibration at the end of the mode is evaluated. A preliminary study was done on a geometrically nonlinear system which also has position-dependency. The system consisted of a flexible four-bar linkage with elastic input and output shafts. The behavior of the rocker-beam is analyzed for different boundary conditions to show how some limiting cases are obtained. A dimensional analysis leads to an evaluation of the consequences of dynamic similarity on the resulting vibration.

Generating Communications Systems Through Shared Context

In a distributed model of intelligence, peer components need to communicate with one another. I present a system which enables two agents connected by a thick twisted bundle of wires to bootstrap a simple communication system from observations of a shared environment. The agents learn a large vocabulary of symbols, as well as inflections on those symbols which allow thematic role-frames to be transmitted. Language acquisition time is rapid and linear in the number of symbols and inflections. The final communication system is robust and performance degrades gradually in the face of problems.

New insights on river water chemistry by using non-centred simplicial principal component analysis: a case study

The use of perturbation and power transformation operations permits the investigation of linear processes in the simplex as in a vectorial space. When the investigated geochemical processes can be constrained by the use of well-known starting point, the eigenvectors of the covariance matrix of a non-centred principal component analysis allow to model compositional changes compared with a reference point. The results obtained for the chemistry of water collected in River Arno (central-northern Italy) have open new perspectives for considering relative changes of the analysed variables and to hypothesise the relative effect of different acting physical-chemical processes, thus posing the basis for a quantitative modelling

Empowerment: model i instrument de mesura basat en les variables primàries o efectives PIEQ (Primary Items Empowerment Questionnaire)

In this thesis a review of the state of the art on empowerment is found. A proposal is put forward for a model of the effective variables of empowerment, a new theoretical model that provides a distinct classification of individual variables. The model consists of four metavariables called reciprocal, unidirectional, shared and reflexive. Finally, a measurement tool for measuring and representing these variables graphically is described, including its process of elaboration through a preliminary pilot study that served to refine and improve the questionnaire. Both the model and the instrument proposed aim to determine the state of the primary variables involved in determining the predisposition and potential of a working group towards empowerment. With the measurement tool both organisational, departmental, working group and/or individual data can be obtained. This instrument can help companies and organisations to discover the limitations existing within a working group and act in consequence.

A deterministic model for lake clarity; application to management of Lake Tahoe (California-Nevada), USA

This dissertation has as its goal the quantitative evaluation of the application of coupled hydrodynamic, ecological and clarity models, to address the deterministic prediction of water clarity in lakes and reservoirs. Prediction of water clarity is somewhat unique, insofar as it represents the integrated and coupled effects of a broad range of individual water quality components. These include the biological components such as phytoplankton, together with the associated cycles of nutrients that are needed to sustain their popuiations, and abiotic components such as suspended particles that may be introduced by streams, atmospheric deposition or sediment resuspension. Changes in clarity induced by either component will feed back on the phytoplankton dynamics, as incident light also affects biological growth. Thus ability to successfully model changes in clarity will by necessity have to achieve the correct modeling of these other water quality parameters. Water clarity is also unique in that it may be one of the earliest and most easily detected wamings of the acceleration of the process of eutrophication in a water body.

A Demographic Model to Evaluate Population Declines in the Endangered Streaked Horned Lark

The Streaked Horned Lark (Eremophila alpestris strigata) is listed as endangered by the State of Washington, USA and by Canada under the Species at Risk Act and is also classified as a federal candidate for listing under the Endangered Species Act in the USA. A substantial portion of Streaked Horned Lark habitat has been lost or degraded, and range contraction has occurred in Oregon, Washington, and British Columbia. We estimate the vital rates (fecundity, adult and juvenile survival) and population growth rate (λ) for Streaked Horned Larks breeding in Washington, USA and conduct a Life-Stage Simulation Analysis (LSA) to evaluate which vital rate has the greatest influence on λ. We simulated changes in the three vital rates to examine how much they would need to be adjusted either independently or in concert to achieve a stable Streaked Horned Lark population (λ = 1). We also evaluated which fecundity component (the number of fledglings per egg laid or renesting interval) had the greatest impact on λ. The estimate of population growth suggests that Streaked Horned Larks in Washington are declining rapidly (λ = 0.62 ± 0.10) and that local breeding sites are not sustainable without immigration. The LSA results indicate that adult survival had the greatest influence on λ, followed by juvenile survival and fecundity. However, increases in vital rates led to λ = 1 only when adult survival was raised from 0.47 to 0.85, juvenile survival from 0.17 to 0.58, and fecundity from 0.91 to 3.09. Increases in breeding success and decreases in the renesting interval influenced λ similarly; however, λ did not reach 1 even when breeding success was raised to 100% or renesting intervals were reduced to 1 day. Only when all three vital rates were increased simultaneously did λ approach 1 without requiring highly unrealistic increases in each vital rate. We conclude that conservation activities need to target all or multiple vital rates to be successful. The baseline data presented here and subsequent efforts to manage Streaked Horned Larks will provide valuable information for management of other declining Horned Lark subspecies and other grassland songbirds across North America.

A simple model of convection with memory

There are at least three distinct time scales that are relevant for the evolution of atmospheric convection. These are the time scale of the forcing mechanism, the time scale governing the response to a steady forcing, and the time scale of the response to variations in the forcing. The last of these, tmem, is associated with convective life cycles, which provide an element of memory in the system. A highly simplified model of convection is introduced, which allows for investigation of the character of convection as a function of the three time scales. For short tmem, the convective response is strongly tied to the forcing as in conventional equilibrium parameterization. For long tmem, the convection responds only to the slowly evolving component of forcing, and any fluctuations in the forcing are essentially suppressed. At intermediate tmem, convection becomes less predictable: conventional equilibrium closure breaks down and current levels of convection modify the subsequent response.

Spatial analysis of the error in a model of soil nitrogen

Models of the dynamics of nitrogen in soil (soil-N) can be used to aid the fertilizer management of a crop. The predictions of soil-N models can be validated by comparison with observed data. Validation generally involves calculating non-spatial statistics of the observations and predictions, such as their means, their mean squared-difference, and their correlation. However, when the model predictions are spatially distributed across a landscape the model requires validation with spatial statistics. There are three reasons for this: (i) the model may be more or less successful at reproducing the variance of the observations at different spatial scales; (ii) the correlation of the predictions with the observations may be different at different spatial scales; (iii) the spatial pattern of model error may be informative. In this study we used a model, parameterized with spatially variable input information about the soil, to predict the mineral-N content of soil in an arable field, and compared the results with observed data. We validated the performance of the N model spatially with a linear mixed model of the observations and model predictions, estimated by residual maximum likelihood. This novel approach allowed us to describe the joint variation of the observations and predictions as: (i) independent random variation that occurred at a fine spatial scale; (ii) correlated random variation that occurred at a coarse spatial scale; (iii) systematic variation associated with a spatial trend. The linear mixed model revealed that, in general, the performance of the N model changed depending on the spatial scale of interest. At the scales associated with random variation, the N model underestimated the variance of the observations, and the predictions were correlated poorly with the observations. At the scale of the trend, the predictions and observations shared a common surface. The spatial pattern of the error of the N model suggested that the observations were affected by the local soil condition, but this was not accounted for by the N model. In summary, the N model would be well-suited to field-scale management of soil nitrogen, but suited poorly to management at finer spatial scales. This information was not apparent with a non-spatial validation. (c),2007 Elsevier B.V. All rights reserved.

Calibration and sensitivity analysis of a river water quality model under unsteady flow conditions

Water quality models generally require a relatively large number of parameters to define their functional relationships, and since prior information on parameter values is limited, these are commonly defined by fitting the model to observed data. In this paper, the identifiability of water quality parameters and the associated uncertainty in model simulations are investigated. A modification to the water quality model `Quality Simulation Along River Systems' is presented in which an improved flow component is used within the existing water quality model framework. The performance of the model is evaluated in an application to the Bedford Ouse river, UK, using a Monte-Carlo analysis toolbox. The essential framework of the model proved to be sound, and calibration and validation performance was generally good. However some supposedly important water quality parameters associated with algal activity were found to be completely insensitive, and hence non-identifiable, within the model structure, while others (nitrification and sedimentation) had optimum values at or close to zero, indicating that those processes were not detectable from the data set examined. (C) 2003 Elsevier Science B.V. All rights reserved.

The physical properties of the atmosphere in the new Hadley Centre Global Environmental Model (HadGEM1). Part II: Aspects of variability and regional climate

The performance of the atmospheric component of the new Hadley Centre Global Environmental Model (HadGEM1) is assessed in terms of its ability to represent a selection of key aspects of variability in the Tropics and extratropics. These include midlatitude storm tracks and blocking activity, synoptic variability over Europe, and the North Atlantic Oscillation together with tropical convection, the Madden-Julian oscillation, and the Asian summer monsoon. Comparisons with the previous model, the Third Hadley Centre Coupled Ocean-Atmosphere GCM (HadCM3), demonstrate that there has been a considerable increase in the transient eddy kinetic energy (EKE), bringing HadGEM1 into closer agreement with current reanalyses. This increase in EKE results from the increased horizontal resolution and, in combination with the improved physical parameterizations, leads to improvements in the representation of Northern Hemisphere storm tracks and blocking. The simulation of synoptic weather regimes over Europe is also greatly improved compared to HadCM3, again due to both increased resolution and other model developments. The variability of convection in the equatorial region is generally stronger and closer to observations than in HadCM3. There is, however, still limited convective variance coincident with several of the observed equatorial wave modes. Simulation of the Madden-Julian oscillation is improved in HadGEM1: both the activity and interannual variability are increased and the eastward propagation, although slower than observed, is much better simulated. While some aspects of the climatology of the Asian summer monsoon are improved in HadGEM1, the upper-level winds are too weak and the simulation of precipitation deteriorates. The dominant modes of monsoon interannual variability are similar in the two models, although in HadCM3 this is linked to SST forcing, while in HadGEM1 internal variability dominates. Overall, analysis of the phenomena considered here indicates that HadGEM1 performs well and, in many important respects, improves upon HadCM3. Together with the improved representation of the mean climate, this improvement in the simulation of atmospheric variability suggests that HadGEM1 provides a sound basis for future studies of climate and climate change.