Optimisation de la cryo microscopie électronique pour les études des minicercles d'ADN

RESUME : Bien que les propriétés physiques de la structure de l'ADN aient été intensivement étudiées pendant plus de 50 ans il y a encore beaucoup de questions importantes qui attendent des réponses. Par exemple, qu'arrive-t-il à la structure de la double hélice d'ADN nue (sans protéines liées) lorsqu'elle est fortement courbée, de la même manière que dans les nucléosomes? Cet ADN nu est-il facilement plié (il reste dans le régime élastique) ou réduit-il la contrainte de flexion en formant des sites hyperflexibles «kinks» (il sort du régime élastique en cassant l'empilement des paires de bases à certains endroits) ? La microscopie électronique peut fournir une réponse à cette question par visualisation directe des minicercles d'ADN de la longueur d'un tour de nucléosome (environ 90 paires de bases). Pour que la réponse soit scientifiquement valide, on doit observer les molécules d'ADN lorsqu'elles sont en suspension dans la solution d'intérêt et sans que des colorations, produits chimiques ou fixatifs n'aient été ajoutés, étant donné que ceux-ci peuvent changer les propriétés de l'ADN. La technique de la cryo-microscopie électronique (cryo-EM) développée par le groupe de Jacques Dubochet au début des années 80, permet la visualisation directe des molécules d'ADN suspendues dans des couche minces vitrifiées de solutions aqueuses. Toutefois, le faible contraste qui caractérise la cryo-EM combinée avec la très petite taille des minicercles d'ADN rendent nécessaire l'optimisation de plusieurs étapes, aussi bien dans la préparation des échantillons que dans le processus d'acquisition d'images afin d'obtenir deux clichés stéréo qui permettent la reconstruction 3-D des minicercles d'ADN. Dans la première partie de ma thèse, je décris l'optimisation de certains paramètres pour la cryoEM et des processus d'acquisition d'image utilisant comme objets de test des plasmides et d'autres molécules d'ADN. Dans la deuxième partie, je .décris comment j'ai construit les minicercles d'ADN de 94 bp et comment j'ai introduit des modifications structurelles comme des coupures ou des lacunes. Dans la troisième partie, je décris l'analyse des reconstructions des rninicercles d'ADN. Cette analyse, appuyée par des tests biochimiques, indique fortement que des molécules d'ADN sont capables de former de petites molécules circulaires de 94 bp sans dépasser les limites d'élasticité, indiquant que les minicercles adoptent une forme circulaire régulière où la flexion est redistribuée le long la molécule. ABSTRACT : Although physical properties of DNA structure have been intensively studied for over 50 years there are still many important questions that need to be answered. For example, what happens to protein-free double-stranded DNA when it is strongly bent, as in DNA forming nucleosomes? Is such protein-free DNA smoothly bent (i.e. it remains within elastic limits of DNA rigidity) or does it release its bending stress by forming sharp kinks (i.e. it exits the elastic regime and breaks the stacking between neighbouring base-pairs in localized regions)? Electron microscopy can provide an answer to this question by directly visualizing DNA minicircles that have the size of nucleosome gyres (ca 90 bp). For the answer to be scientifically valid, one needs to observe DNA molecules while they are still suspended in the solution of interest and no staining chemicals or fixatives have been added since these can change the properties of the DNA. CryoEM techniques developed by Jacques Dubochet's group beginning in the 1980's permit direct visualization of DNA molecules suspended in cryo-vitrified layers of aqueous solutions. However, a relatively weak contrast of cryo-EM preparations combined with the very small size of the DNA minicircles made it necessary to optimize many of the steps and parameters of the cryo-EM specimen preparation and image acquisition processes in order to obtain stereo-pairs of images that permit the 3-D reconstruction of the observed DNA minicircles. In the first part of my thesis I describe the optimization of the cryo-EM preparation and the image acquisition processes using plasmid size DNA molecules as a test object. In the second part, I describe how I formed the 94 by DNA minicircles and how I introduced structural modifications like nicks or gaps. In the third part, I describe the cryo-EM analysis of the constructed DNA minicircles. That analysis, supported by biochemical tests, strongly indicates that DNA minicircles as small as 94 by remain within the elastic limits of DNA structure, i.e. the minicircles adopt a regular circular shape where bending is redistributed along the molecules.

Physiopathologie du coeur embryonnaire soumis à l'anoxie-réoxygénation: rôle protecteur du NO et des canaux KATP

RESUME Introduction : Dans le coeur adulte, l'ischémie et la reperfusion entraînent des perturbations électriques, mécaniques, biochimiques et structurales qui peuvent causer des dommages réversibles ou irréversibles selon la sévérité de l'ischémie. Malgré les récents progrès en cardiologie et en chirurgie foetales, la connaissance des mécanismes impliqués dans la réponse du myocarde embryonnaire à un stress hypoxique transitoire demeure lacunaire. Le but de ce travail a donc été de caractériser les effets chrono-, dromo- et inotropes de l'anoxie et de la réoxygénation sur un modèle de coeur embryonnaire isolé. D'autre part, les effets du monoxyde d'azote (NO) et de la modulation des canaux KATP mitochondriaux (mito KATP) sur la récupération fonctionnelle postanoxique ont été étudiés. La production myocardique de radicaux d'oxygène (ROS) et l'activité de MAP Kinases (ERK et JNK) impliquées dans la signalisation cellulaire ont également été déterminées. Méthodes : Des coeurs d'embryons de poulet âgés de 4 jours battant spontanément ont été placés dans une chambre de culture puis soumis à une anoxie de 30 min suivie d'une réoxygénation de 60 min. L'activité électrique (ECG), les contractions de l'oreillette, du ventricule et du conotroncus (détectées par photométrie), la production de ROS (mesure de la fluorescence du DCFH) et l'activité kinase de ERK et JNK dans le ventricule ont été déterminées au cours de l'anoxie et de la réoxygénation. Les coeurs ont été traités avec un bloqueur des NO synthases (L-NAME), un donneur de NO (DETA-NONOate), un activateur (diazoxide) ou un inhibiteur (5-HD) des canaux mitoKATP un inhibiteur non-spécifique des PKC (chélérythrine) ou un piégeur de ROS (MPG). Résultats : L'anoxie et la réoxygénation entraînaient des arythmies (essentiellement d'origine auriculaire) semblables à celles observées chez l'adulte, des troubles de la conduction (blocs auriculo-ventriculaires de 1er, 2ème et 3ème degré) et un ralentissement marqué du couplage excitation-contraction (E-C) ventriculaire. En plus de ces arythmies, la réoxygénation déclenchait le phénomène de Wenckelbach, de rares échappements ventriculaires et une sidération myocardique. Aucune fibrillation, conduction rétrograde ou activité ectopique n'ont été observées. Le NO exogène améliorait la récupération postanoxique du couplage E-C ventriculaire alors que L'inhibition des NOS la ralentissait. L'activation des canaux mito KATP augmentait la production mitochondriale de ROS à la réoxygénation et accélérait la récupération de la conduction (intervalle PR) et du couplage E-C ventriculaire. La protection de ce couplage était abolie par le MPG, la chélérythrine ou le L-NAME. Les fonctions électrique et contractile de tous les coeurs récupéraient après 30-40 min de réoxygénation. L'activité de ERK et de JNK n'était pas modifiée par L'anoxie, mais doublait et quadruplait, respectivement, après 30 min de réoxygénation. Seule l'activité de JNK était diminuée (-60%) par l'activation des canaux mitoKATP. Cet effet inhibiteur était partiellement abolit par le 5-HD. Conclusion: Dans le coeur immature, le couplage E-C ventriculaire semble être un paramètre particulièrement sensible aux conditions d'oxygénation. Sa récupération postanoxique est améliorée par l'ouverture des canaux mitoKATP via une signalisation impliquant les ROS Ies PKC et le NO. Une réduction de l'activité de JNK semble également participer à cette protection. Nos résultats suggèrent que les mitochondries jouent un rôle central dans la modulation des voies de signalisation cellulaire, en particulier lorsque les conditions métaboliques deviennent défavorables. Le coeur embryonnaire isolé représente donc un modèle expérimental utile pour mieux comprendre les mécanismes associés à une hypoxie in utero et pour améliorer les stratégies thérapeutiques en cardiologie et chirurgie foetales. ABSTRACT Physiopathology of the anoxic-reoxygenated embryonic heart: Protective role of NO and KATP channel Aim: In the adult heart, the electrical, mechanical, biochemical and structural disturbances induced by ischemia and reperfusion lead to reversible or irreversible damages depending on the severity and duration of ischemia. In spite of recent advances in fetal cardiology and surgery, little is known regarding the cellular mechanisms involved in hypoxia-induced dysfunction in the developing heart. The aim of this study was to precisely characterize the chrono-, dromo- and inotropic disturbances associated with anoxia-reoxygenation in an embryonic heart model. Furthermore, the roles that nitric oxide (NO), reactive oxygen species (ROS), mitochondrial KATP, (mito KATP) channel and MAP Kinases could play in the stressed developing heart have been investigated. Methods: Embryonic chick hearts (4-day-old) were isolated and submitted in vitro to 30 min anoxia followed by 60 min reoxygenation. Electrical (ECG) and contractile activities of atria, ventricle and conotruncus (photometric detection), ROS production (DCFH fluorescence) and ERK and JNK activity were determined in the ventricle throughout anoxia-reoxygenation. Hearts were treated with NO synthase inhibitor (L-NAME), NO donor (DETA-NONOate), mitoKATP channel opener (diazoxide) or blocket (5-HD), PKC inhibitor (chelerythrine) and ROS scavenger (MPG). Results: Anoxia and reoxygenation provoked arrhythxnias (mainly originating from atrial region), troubles of conduction (st, 2nd, and 3rd degree atrio-ventricular blocks) and disturbances of excitation-contraction (E-C) coupling. In addition to these types of arrhythmias, reoxygenation triggered Wenckebach phenomenon and rare ventricular escape beats. No fibrillations, no ventricular ectopic beats and no electromechanical dissociation were observed. Myocardial stunning was observed during the first 30 min of reoxygenation. All hearts fully recovered their electrical and mechanical functions after 30-40 min of reoxygenation. Exogenous NO improved while NOS inhibition delayed E-C coupling recovery. Mito KATP, channel opening increased reoxygenation-induced ROS production and improved E-C coupling and conduction (PR) recovery. MPG, chelerythrine or L-NAME reversed this effect. Reoxygenation increased ERK and JNK activities land 4-fold, respectively, while anoxia had no effect. MitoKATP channel opening abolished the reoxygenation-induced activation of JNK but had no effect on ERK activity. This inhibitory effect was partly reversed by mitoKATP channel blocker but not by MPG. Conclusion: In the developing heart, ventricular E-C coupling was found to be specially sensitive to hypoxia-reoxygenation and its postanoxic recovery was improved by mitoKATP channel activation via a ROS-, PKC- and NO-dependent pathway. JNK inhibition appears to be involved in this protection. Thus, mitochondria can play a pivotal role in the cellular signalling pathways, notably under critical metabolic conditions. The model of isolated embryonic heart appears to be useful to better understand the mechanisms underlying the myocardial dysfunction induced by an in utero hypoxia and to improve therapeutic strategies in fetal cardiology and surgery.

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Retinoid X Receptors (RXR) were initially identified as nuclear receptors binding with stereo-selectivity the vitamin A derivative 9-cis retinoic acid, although the relevance of this molecule as endogenous activator of RXRs is still elusive. Importantly, within the nuclear receptor superfamily, RXRs occupy a peculiar place, as they are obligatory partners for a number of other nuclear receptors, thus integrating the corresponding signaling pathways. In this chapter, we describe the structural features allowing RXR to form homo- and heterodimers, and the functional consequences of this unique ability. Furthermore, we discuss the importance of studying RXR activity at a genome-wide level in order to comprehensively address the biological implications of their action that is fundamental to understand to what extent RXRs could be exploited as new therapeutic targets.

Analysis of the alternative pathways for the beta-oxidation of unsaturated fatty acids using transgenic plants synthesizing polyhydroxyalkanoates in peroxisomes.

Degradation of fatty acids having cis-double bonds on even-numbered carbons requires the presence of auxiliary enzymes in addition to the enzymes of the core beta-oxidation cycle. Two alternative pathways have been described to degrade these fatty acids. One pathway involves the participation of the enzymes 2, 4-dienoyl-coenzyme A (CoA) reductase and Delta(3)-Delta(2)-enoyl-CoA isomerase, whereas the second involves the epimerization of R-3-hydroxyacyl-CoA via a 3-hydroxyacyl-CoA epimerase or the action of two stereo-specific enoyl-CoA hydratases. Although degradation of these fatty acids in bacteria and mammalian peroxisomes was shown to involve mainly the reductase-isomerase pathway, previous analysis of the relative activity of the enoyl-CoA hydratase II (also called R-3-hydroxyacyl-CoA hydro-lyase) and 2,4-dienoyl-CoA reductase in plants indicated that degradation occurred mainly through the epimerase pathway. We have examined the implication of both pathways in transgenic Arabidopsis expressing the polyhydroxyalkanoate synthase from Pseudomonas aeruginosa in peroxisomes and producing polyhydroxyalkanoate from the 3-hydroxyacyl-CoA intermediates of the beta-oxidation cycle. Analysis of the polyhydroxyalkanoate synthesized in plants grown in media containing cis-10-heptadecenoic or cis-10-pentadecenoic acids revealed a significant contribution of both the reductase-isomerase and epimerase pathways to the degradation of these fatty acids.

Three-stranded DNA structure; is this the secret of DNA homologous recognition?

A novel type of triple-stranded DNA structure was proposed by several groups to play a crucial role in homologous recognition between single- and double-stranded DNA molecules. In this still putative structure a duplex DNA was proposed to co-ordinate a homologous single strand in its major groove side. In contrast to the well-characterized pyrimidine-purine-pyrimidine triplexes in which the two like strands are antiparallel and which are restricted to poly-pyrimidine-containing stretches, the homology-specific triplexes would have like strands in parallel orientation and would not be restricted to any particular sequence provided that there is a homology between interacting DNA molecules. For many years the stereo-chemical possibility of forming homology-dependent three- or four-stranded DNA structures during the pairing stage of recombination reactions was seriously considered in published papers. However, only recently has there been a marked increase in the number of papers that have directly tested the formation of triple-stranded DNA structures during the actual pairing stage of the recombination reaction. Unfortunately the results of these tests are not totally clear cut; while some laboratories presented experimental evidence consistent with the formation of triplexes, others studying the same or very similar systems offered alternative explanations. The aim of this review is to present the current state of the central question in the mechanism of homologous recombination, namely, what kind of DNA structure is responsible for DNA homologous recognition. Is it a novel triplex structure or just a classical duplex?

Spatial visualization of DNA in solution.

An image analysis method is presented which allows for the reconstruction of the three-dimensional path of filamentous objects from two of their projections. Starting with stereo pairs, this method is used to trace the trajectory of DNA molecules embedded in vitreous ice and leads to a faithful representation of their three-dimensional shape in solution. This computer-aided reconstruction is superior to the subjective three-dimensional impression generated by observation of stereo pairs of micrographs because it enables one to look at the reconstructed molecules from any chosen direction and distance and allows quantitative analysis such as determination of distances, curvature, persistence length, and writhe of DNA molecules in solution.

Fatigue resistance of denture teeth

AIMS: There is no standard test to determine the fatigue resistance of denture teeth. With the increasing number of patients with implant-retained dentures the mechanical strength of the denture teeth requires more attention and valid laboratory test set-ups. The purpose of the present study was to determine the fatigue resistance of various denture teeth using a dynamic load testing machine. METHODS: Four denture teeth were used: Bonartic II (Candulor), Physiodens (Vita), SR Phonares II (Ivoclar Vivadent) and Trubyte (Dentsply). For dynamic load testing, first upper molars with a similar shape and cusp inclination were selected. The molar teeth were embedded in cylindrical steel molds with denture base material (ProBase, Ivoclar Vivadent). Dynamic fatigue loading was carried out on the mesio-buccal cusp at a 45° angle using dynamic testing machines and 2,000,000 cycles at 2Hz in water (37°C). Three specimens per group and load were submitted to decreasing load levels (at least 4) until all the three specimens no longer showed any failures. All the specimens were evaluated under a stereo microscope (20× magnification). The number of cycles reached before observing a failure, and its dependence on the load and on the material, has been modeled using a parametric survival regression model with a lognormal distribution. This allowed to estimate the fatigue resistance for a given material as the maximal load for which one would observe less than 1% failure after 2,000,000 cycles. RESULTS: The failure pattern was similar for all denture teeth, showing a large chipping of the loaded mesio-buccal cusp. In our regression model, there were statistically significant differences among the different materials, with SR Phonares II and Bonartic II showing a higher resistance than Physiodens and Trubyte, the fatigue resistance being estimated at around 110N for the former two, and at about 60N for the latter two materials. CONCLUSION: The fatigue resistance may be a useful parameter to assess and to compare the clinical risk of chipping and fracture of denture tooth materials.