Interactions protéiques et relation dynamique entre phosphorylation / sumoylation / ubiquitination des protéines TIF1α, β et PML: détection in vivo par BRET

Trois protéines de la famille TRIM (Motif TRIpartite), TIF1α, β (Transcriptional Intermediary Factor 1) et PML (ProMyelocytic Leukaemia¬), font l’objet de cette étude. TIF1α est connu comme un coactivateur des récepteurs nucléaires et TIF1β comme le corépresseur universel des protéines KRAB-multidoigt de zinc dont le prototype étudié ici est ZNF74. PML possède divers rôles dont le plus caractérisé est celui d’être l’organisateur principal et essentiel des PML-NBs (PML-Nuclear Bodies), des macrostructures nucléaires très dynamiques regroupant et coordonnant plus de 40 protéines. Il est à noter que la fonction de TIF1α, β et PML est régulée par une modification post-traductionnelle, la sumoylation, qui implique le couplage covalent de la petite protéine SUMO (Small Ubiquitin like MOdifier) à des lysines de ces trois protéines cibles. Cette thèse propose de développer des méthodes utilisant le BRET (Bioluminescence Resonance Energy Transfert) afin de détecter dans des cellules vivantes et en temps réel des interactions non-covalentes de protéines nucléaires mais aussi leur couplage covalent à SUMO. En effet, le BRET n’a jamais été exploré jusqu’alors pour étudier les interactions non-covalentes et covalentes de protéines nucléaires. L’étude de l’interaction de protéines transcriptionnellement actives est parfois difficile par des méthodes classiques du fait de leur grande propension à agréger (famille TRIM) ou de leur association à la matrice nucléaire (ZNF74). L’homo et l’hétérodimérisation de TIF1α, β ainsi que leur interaction avec ZNF74 sont ici testées sur des protéines entières dans des cellules vivantes de mammifères répondant aux résultats conflictuels de la littérature et démontrant que le BRET peut être avantageusement utilisé comme alternative aux essais plus classiques basés sur la transcription. Du fait de l’hétérodimérisation confirmée de TIF1α et β, le premier article présenté ouvre la possibilité d’une relation étroite entre les récepteurs nucléaires et les protéines KRAB- multidoigt de zinc. Des études précédentes ont démontré que la sumoylation de PML est impliquée dans sa dégradation induite par l’As2O3 et dépendante de RNF4, une E3 ubiquitine ligase ayant pour substrat des chaînes de SUMO (polySUMO). Dans le second article, grâce au développement d’une nouvelle application du BRET pour la détection d’interactions covalentes et non-covalentes avec SUMO (BRETSUMO), nous établissons un nouveau lien entre la sumoylation de PML et sa dégradation. Nous confirmons que le recrutement de RNF4 dépend de SUMO mais démontrons également l’implication du SBD (Sumo Binding Domain) de PML dans sa dégradation induite par l’As2O3 et/ou RNF4. De plus, nous démontrons que des sérines, au sein du SBD de PML, qui sont connues comme des cibles de phosphorylation par la voie de la kinase CK2, régulent les interactions non-covalentes de ce SBD mettant en évidence, pour la première fois, que les interactions avec un SBD peuvent dépendre d’un évènement de phosphorylation (“SBD phospho-switch”). Nos résultats nous amènent à proposer l’hypothèse que le recrutement de PML sumoylé au niveau des PML-NBs via son SBD, favorise le recrutement d’une autre activité E3 ubiquitine ligase, outre celle de RNF4, PML étant lui-même un potentiel candidat. Ceci suggère l’existence d’une nouvelle relation dynamique entre phosphorylation, sumoylation et ubiquitination de PML. Finalement, il est suggéré que PML est dégradé par deux voies différentes dépendantes de l’ubiquitine et du protéasome; la voie de CK2 et la voie de RNF4. Enfin une étude sur la sumoylation de TIF1β est également présentée en annexe. Cette étude caractérise les 6 lysines cibles de SUMO sur TIF1β et démontre que la sumoylation est nécessaire à l’activité répressive de TIF1β mais n’est pas impliquée dans son homodimérisation ou son interaction avec la boîte KRAB. La sumoylation est cependant nécessaire au recrutement d’histones déacétylases, dépendante de son homodimérisation et de l’intégrité du domaine PHD. Alors que l’on ne connaît pas de régulateur physiologique de la sumoylation outre les enzymes directement impliquées dans la machinerie de sumoylation, nous mettons en évidence que la sumoylation de TIF1β est positivement régulée par son interaction avec le domaine KRAB et suggérons que ces facteurs transcriptionnels recrutent TIF1β à l’ADN au niveau de promoteur et augmentent son activité répressive en favorisant sa sumoylation.

Représentation de trajectoires spatiotemporelles dans un système d’information géographique : le cas des activités d’observation de mammifères marins dans le Parc marin du Saguenay – Saint-Laurent

Parc marin du Saguenay - Saint-Laurent, Groupe de recherche et d'éducation sur les mammifères marins, GREMM, excursions aux baleines, bélugas, Tadoussac, règlementation, ArcCatalog, ArcMap.

Auditory and visual event-related potential alterations in fragile X syndrome

Le syndrome du X fragile (SXF) est la première cause héréditaire de déficience intellectuelle et également la première cause monogénique d’autisme. Le SXF est causé par l'expansion de la répétition du nucléotide CGG sur le gène FMR1, ce qui empêche l’expression de la protéine FMRP. L’absence du FMRP mène à une altération du développement structurel et fonctionnel de la synapse, ce qui empêche la maturation des synapses induite par l’activité et l’élagage synaptique, qui sont essentiels pour le développement cérébral et cognitif. Nous avons investigué les potentiels reliés aux événements (PRE) évoqués par des stimulations fondamentales auditives et visuelles dans douze adolescents et jeunes adultes (10-22) atteints du SXF, ainsi que des participants contrôles appariés en âge chronologique et développemental. Les résultats indiquent un profil des PRE altéré, notamment l’augmentation de l’amplitude de N1 auditive, par rapport aux deux groupes contrôle, ainsi que l’augmentation des amplitudes de P2 et N2 auditifs et de la latence de N2 auditif. Chez les patients SXF, le traitement sensoriel semble être davantage perturbé qu’immature. En outre, la modalité auditive semble être plus perturbée que la modalité visuelle. En combinaison avec des résultats anatomique du cerveau, des mécanismes biochimiques et du comportement, nos résultats suggèrent une hyperexcitabilité du système nerveux dans le SXF.

Carbon/Nitrogen Ratio Optimization and Periphyton Development on the Production and Sustainability of Penaeus Monodon(Fabricius)in Extensive Culture System

Controlling the inorganic nitrogen by manipulating carbon / nitrogen ratio is a method gaining importance in aquaculture systems. Nitrogen control is induced by feeding bacteria with carbohydrates and through the subsequent uptake of nitrogen from the water for the synthesis of microbial proteins. The relationship between addition of carbohydrates, reduction of ammonium and the production of microbial protein depends on the microbial conversion coefficient. The carbon / nitrogen ratio in the microbial biomass is related to the carbon contents of the added material. The addition of carbonaceous substrate was found to reduce inorganic nitrogen in shrimp culture ponds and the resultant microbial proteins are taken up by shrimps. Thus, part of the feed protein is replaced and feeding costs are reduced in culture systems.The use of various locally available substrates for periphyton based aquaculture practices increases production and profitability .However, these techniques for extensive shrimp farming have not so far been evaluated. Moreover, an evaluation of artificial substrates together with carbohydrate source based farming system in reducing inorganic nitrogen production in culture systems has not yet been carried-out. Furthermore, variations in water and soil quality, periphyton production and shrimp production of the whole system have also not been determined so-far.This thesis starts with a general introduction , a brief review of the most relevant literature, results of various experiments and concludes with a summary (Chapter — 9). The chapters are organised conforming to the objectives of the present study. The major objectives of this thesis are, to improve the sustainability of shrimp farming by carbohydrate addition and periphyton substrate based shrimp production and to improve the nutrient utilisation in aquaculture systems.

Development of Total Quality Management System in Seafood (Freezing) Industry in Kerala

Quality related problems have become dominant in the seafood processing industry in Kerala. This has resulted in the rejection of seafood sent from India to many destinations. The latest being the total block listing of seafood companies from India from being exported to Europe and partial block listing by the US. The quality systems prevailed in the seafood industry in India were outdated and no longer in use in the developed world. According to EC Directive discussed above all the seafood factories exporting to European countries have to adopt HACCP. Based on this, EIA has now made HACCP system mandatory in all the seafood processing factories in India. This transformation from a traditional product based inspection system to a process control system requires thorough changes in the various stages of production and quality management. This study is conducted by the author with to study the status of the existing infrastructure and quality control system in the seafood industry in Kerala with reference to the recent developments in the quality concepts in international markets and study the drawbacks, if any, of the existing quality management systems in force in the seafood factories in Kerala for introducing the mandatory HACCP concept. To assess the possibilities of introducing Total Quality Management system in the seafood industry in Kerala in order to effectively adopt the HACCP concept. This is also aimed at improving the quality of the products and productivity of the industry by sustaining the world markets in the long run.

A Realization Of An Fpga Sub System For Reducing Odometric Localization Errors In Wheeled Mobile Robots

This paper introduces a simple and efficient method and its implementation in an FPGA for reducing the odometric localization errors caused by over count readings of an optical encoder based odometric system in a mobile robot due to wheel-slippage and terrain irregularities. The detection and correction is based on redundant encoder measurements. The method suggested relies on the fact that the wheel slippage or terrain irregularities cause more count readings from the encoder than what corresponds to the actual distance travelled by the vehicle. The standard quadrature technique is used to obtain four counts in each encoder period. In this work a three-wheeled mobile robot vehicle with one driving-steering wheel and two-fixed rear wheels in-axis, fitted with incremental optical encoders is considered. The CORDIC algorithm has been used for the computation of sine and cosine terms in the update equations. The results presented demonstrate the effectiveness of the technique

Improved Biometric Authentication System Using Multimodal Cue Integration

Biometrics is an efficient technology with great possibilities in the area of security system development for official and commercial applications. The biometrics has recently become a significant part of any efficient person authentication solution. The advantage of using biometric traits is that they cannot be stolen, shared or even forgotten. The thesis addresses one of the emerging topics in Authentication System, viz., the implementation of Improved Biometric Authentication System using Multimodal Cue Integration, as the operator assisted identification turns out to be tedious, laborious and time consuming. In order to derive the best performance for the authentication system, an appropriate feature selection criteria has been evolved. It has been seen that the selection of too many features lead to the deterioration in the authentication performance and efficiency. In the work reported in this thesis, various judiciously chosen components of the biometric traits and their feature vectors are used for realizing the newly proposed Biometric Authentication System using Multimodal Cue Integration. The feature vectors so generated from the noisy biometric traits is compared with the feature vectors available in the knowledge base and the most matching pattern is identified for the purpose of user authentication. In an attempt to improve the success rate of the Feature Vector based authentication system, the proposed system has been augmented with the user dependent weighted fusion technique.

Development of directly modulated high speed telecommunication lasers based on surface defined feedback gratings

High-speed semiconductor lasers are an integral part in the implemen- tation of high-bit-rate optical communications systems. They are com- pact, rugged, reliable, long-lived, and relatively inexpensive sources of coherent light. Due to the very low attenuation window that exists in the silica based optical fiber at 1.55 μm and the zero dispersion point at 1.3 μm, they have become the mainstay of optical fiber com- munication systems. For the fabrication of lasers with gratings such as, distributed bragg reflector or distributed feedback lasers, etching is the most critical step. Etching defines the lateral dimmensions of the structure which determines the performance of optoelectronic devices. In this thesis studies and experiments were carried out about the exist- ing etching processes for InP and a novel dry etching process was de- veloped. The newly developed process was based on Cl2/CH4/H2/Ar chemistry and resulted in very smooth surfaces and vertical side walls. With this process the grating definition was significantly improved as compared to other technological developments in the respective field. A surface defined grating definition approach is used in this thesis work which does not require any re-growth steps and makes the whole fabrication process simpler and cost effective. Moreover, this grating fabrication process is fully compatible with nano-imprint lithography and can be used for high throughput low-cost manufacturing. With usual etching techniques reported before it is not possible to etch very deep because of aspect ratio dependent etching phenomenon where with increasing etch depth the etch rate slows down resulting in non-vertical side walls and footing effects. Although with our de- veloped process quite vertical side walls were achieved but footing was still a problem. To overcome the challenges related to grating defini- tion and deep etching, a completely new three step gas chopping dry etching process was developed. This was the very first time that a time multiplexed etching process for an InP based material system was demonstrated. The developed gas chopping process showed extra ordinary results including high mask selectivity of 15, moderate etch- ing rate, very vertical side walls and a record high aspect ratio of 41. Both the developed etching processes are completely compatible with nano imprint lithography and can be used for low-cost high-throughput fabrication. A large number of broad area laser, ridge waveguide laser, distributed feedback laser, distributed bragg reflector laser and coupled cavity in- jection grating lasers were fabricated using the developed one step etch- ing process. Very extensive characterization was done to optimize all the important design and fabrication parameters. The devices devel- oped have shown excellent performance with a very high side mode suppression ratio of more than 52 dB, an output power of 17 mW per facet, high efficiency of 0.15 W/A, stable operation over temperature and injected currents and a threshold current as low as 30 mA for almost 1 mm long device. A record high modulation bandwidth of 15 GHz with electron-photon resonance and open eye diagrams for 10 Gbps data transmission were also shown.

Image Based Rendering Using Algebraic Techniques

This paper presents an image-based rendering system using algebraic relations between different views of an object. The system uses pictures of an object taken from known positions. Given three such images it can generate "virtual'' ones as the object would look from any position near the ones that the two input images were taken from. The extrapolation from the example images can be up to about 60 degrees of rotation. The system is based on the trilinear constraints that bind any three view so fan object. As a side result, we propose two new methods for camera calibration. We developed and used one of them. We implemented the system and tested it on real images of objects and faces. We also show experimentally that even when only two images taken from unknown positions are given, the system can be used to render the object from other view points as long as we have a good estimate of the internal parameters of the camera used and we are able to find good correspondence between the example images. In addition, we present the relation between these algebraic constraints and a factorization method for shape and motion estimation. As a result we propose a method for motion estimation in the special case of orthographic projection.

Model-based objects recognition in industrial environments for autonomous vehicles control

Behavior-based navigation of autonomous vehicles requires the recognition of the navigable areas and the potential obstacles. In this paper we describe a model-based objects recognition system which is part of an image interpretation system intended to assist the navigation of autonomous vehicles that operate in industrial environments. The recognition system integrates color, shape and texture information together with the location of the vanishing point. The recognition process starts from some prior scene knowledge, that is, a generic model of the expected scene and the potential objects. The recognition system constitutes an approach where different low-level vision techniques extract a multitude of image descriptors which are then analyzed using a rule-based reasoning system to interpret the image content. This system has been implemented using a rule-based cooperative expert system

Model-based objects recognition in man-made environments

We describe a model-based objects recognition system which is part of an image interpretation system intended to assist autonomous vehicles navigation. The system is intended to operate in man-made environments. Behavior-based navigation of autonomous vehicles involves the recognition of navigable areas and the potential obstacles. The recognition system integrates color, shape and texture information together with the location of the vanishing point. The recognition process starts from some prior scene knowledge, that is, a generic model of the expected scene and the potential objects. The recognition system constitutes an approach where different low-level vision techniques extract a multitude of image descriptors which are then analyzed using a rule-based reasoning system to interpret the image content. This system has been implemented using CEES, the C++ embedded expert system shell developed in the Systems Engineering and Automatic Control Laboratory (University of Girona) as a specific rule-based problem solving tool. It has been especially conceived for supporting cooperative expert systems, and uses the object oriented programming paradigm

Application of a support system to the design of wastewater treatment plants

This paper presents a case study that explores the advantages that can be derived from the use of a design support system during the design of wastewater treatment plants (WWTP). With this objective in mind a simplified but plausible WWTP design case study has been generated with KBDS, a computer-based support system that maintains a historical record of the design process. The study shows how, by employing such a historical record, it is possible to: (1) rank different design proposals responding to a design problem; (2) study the influence of changing the weight of the arguments used in the selection of the most adequate proposal; (3) take advantage of keywords to assist the designer in the search of specific items within the historical records; (4) evaluate automatically the compliance of alternative design proposals with respect to the design objectives; (5) verify the validity of previous decisions after the modification of the current constraints or specifications; (6) re-use the design records when upgrading an existing WWTP or when designing similar facilities; (7) generate documentation of the decision making process; and (8) associate a variety of documents as annotations to any component in the design history. The paper also shows one possible future role of design support systems as they outgrow their current reactive role as repositories of historical information and start to proactively support the generation of new knowledge during the design process

A proposal for the diagnosis of uncertain dynamic systems based on interval models

The performance of a model-based diagnosis system could be affected by several uncertainty sources, such as,model errors,uncertainty in measurements, and disturbances. This uncertainty can be handled by mean of interval models.The aim of this thesis is to propose a methodology for fault detection, isolation and identification based on interval models. The methodology includes some algorithms to obtain in an automatic way the symbolic expression of the residual generators enhancing the structural isolability of the faults, in order to design the fault detection tests. These algorithms are based on the structural model of the system. The stages of fault detection, isolation, and identification are stated as constraint satisfaction problems in continuous domains and solved by means of interval based consistency techniques. The qualitative fault isolation is enhanced by a reasoning in which the signs of the symptoms are derived from analytical redundancy relations or bond graph models of the system. An initial and empirical analysis regarding the differences between interval-based and statistical-based techniques is presented in this thesis. The performance and efficiency of the contributions are illustrated through several application examples, covering different levels of complexity.

Case based reasoning as an extension of fault dictionary methods for linear electronic analog circuits diagnosis

El test de circuits és una fase del procés de producció que cada vegada pren més importància quan es desenvolupa un nou producte. Les tècniques de test i diagnosi per a circuits digitals han estat desenvolupades i automatitzades amb èxit, mentre que aquest no és encara el cas dels circuits analògics. D'entre tots els mètodes proposats per diagnosticar circuits analògics els més utilitzats són els diccionaris de falles. En aquesta tesi se'n descriuen alguns, tot analitzant-ne els seus avantatges i inconvenients. Durant aquests últims anys, les tècniques d'Intel·ligència Artificial han esdevingut un dels camps de recerca més importants per a la diagnosi de falles. Aquesta tesi desenvolupa dues d'aquestes tècniques per tal de cobrir algunes de les mancances que presenten els diccionaris de falles. La primera proposta es basa en construir un sistema fuzzy com a eina per identificar. Els resultats obtinguts son força bons, ja que s'aconsegueix localitzar la falla en un elevat tant percent dels casos. Per altra banda, el percentatge d'encerts no és prou bo quan a més a més s'intenta esbrinar la desviació. Com que els diccionaris de falles es poden veure com una aproximació simplificada al Raonament Basat en Casos (CBR), la segona proposta fa una extensió dels diccionaris de falles cap a un sistema CBR. El propòsit no és donar una solució general del problema sinó contribuir amb una nova metodologia. Aquesta consisteix en millorar la diagnosis dels diccionaris de falles mitjançant l'addició i l'adaptació dels nous casos per tal d'esdevenir un sistema de Raonament Basat en Casos. Es descriu l'estructura de la base de casos així com les tasques d'extracció, de reutilització, de revisió i de retenció, fent èmfasi al procés d'aprenentatge. En el transcurs del text s'utilitzen diversos circuits per mostrar exemples dels mètodes de test descrits, però en particular el filtre biquadràtic és l'utilitzat per provar les metodologies plantejades, ja que és un dels benchmarks proposats en el context dels circuits analògics. Les falles considerades son paramètriques, permanents, independents i simples, encara que la metodologia pot ser fàcilment extrapolable per a la diagnosi de falles múltiples i catastròfiques. El mètode es centra en el test dels components passius, encara que també es podria extendre per a falles en els actius.

Integration of knowledge-based, qualitative and numeric tools for real time dynamic systems supervision

The proposal presented in this thesis is to provide designers of knowledge based supervisory systems of dynamic systems with a framework to facilitate their tasks avoiding interface problems among tools, data flow and management. The approach is thought to be useful to both control and process engineers in assisting their tasks. The use of AI technologies to diagnose and perform control loops and, of course, assist process supervisory tasks such as fault detection and diagnose, are in the scope of this work. Special effort has been put in integration of tools for assisting expert supervisory systems design. With this aim the experience of Computer Aided Control Systems Design (CACSD) frameworks have been analysed and used to design a Computer Aided Supervisory Systems (CASSD) framework. In this sense, some basic facilities are required to be available in this proposed framework: ·