The Molecular Basis for Antimicrobial Activity of Pore-Forming Cyclic Peptides

The mechanism of action of antimicrobial peptides is, to our knowledge, still poorly understood. To probe the biophysical characteristics that confer activity, we present here a molecular-dynamics and biophysical study of a cyclic antimicrobial peptide and its inactive linear analog. In the simulations, the cyclic peptide caused large perturbations in the bilayer and cooperatively opened a disordered toroidal pore, 1–2 nm in diameter. Electrophysiology measurements confirm discrete poration events of comparable size. We also show that lysine residues aligning parallel to each other in the cyclic but not linear peptide are crucial for function. By employing dual-color fluorescence burst analysis, we show that both peptides are able to fuse/aggregate liposomes but only the cyclic peptide is able to porate them. The results provide detailed insight on the molecular basis of activity of cyclic antimicrobial peptides

SOURCE, FATE AND FUNCTION OF EARLY GLIAL CELLS EXPRESSING NKX2.1 IN MOUSE EMBRYONIC BRAINS

The brain tissue is made of neuronal and glial cells generated in the germinal layer bordering the ventricles. These cells divide, differentiate and migrate following specific pathways. The specification of GABAergic interneurons and glutamatergic neurons has been broadly studied but little is known about the origin, the fate and the function of early glial cells in the embryonic telencephalon. It has been commonly accepted since long that the glial cells and more particularly the astrocytes were generated after neurogenesis from the dorsal telencephalon. However, our work shows that, unlike what was previously thought, numerous glial cells (astroglia and polydendrocytes) are generated during neurogenesis in the early embryonic stages from E14.5 to E16.5, and originate from the ventral Nkx2.1-expressing precursors instead. NK2 homeobox 1 (Nkx2.1) is a member of the NK2 family of homeodomaincontaining transcription factors. The specification of the MGE precursors requires the expression of the Nkx2.1 homeobox gene. Moreover, Nkx2.1 is previously known to regulate the specification of GABAergic interneurons and early oligodendrocytes in the ventral telencephalon. Here, in my thesis work, I have discovered that, in addition, Nkx2.1 also regulates astroglia and polydendrocytes differentiation. The use of Nkx2.1 antibody and Nkx2.1 riboprobe have revealed the presence of numerous Nkx2.1-positive cells that express astroglial markers (like GLAST and GFAP) in the entire embryonic brain. Thus, to selectively fate map MGE-derived GABAergic interneurons and glia, we crossed Nkx2.1-Cre mice, Glast-Cre ERT+/- inducible mice and NG2-Cre mice with the Cre reporter Rosa26-lox-STOP-lox-YFP (Rosa26-YFP) mice. The precise origin of Nkx2.1-positive astroglia has been directly ascertained by combining glial immunostaining and focal electroporation of the pCAG-GS-EGFP plasmids into the subpallial domains of organotypic slices, as well as, by using in vitro neurosphere experiments and in utero electroporation of the pCAG-GS-tomato plasmid into the ventral pallium of E14.5 Nkx2.1-Cre+/Rosa-YFP+/- embryos. We have, thus, confirmed that the three germinal regions of the ventral telencephalon i.e. the MGE, the AEP/POA and the triangular septal nucleus are able to generate early astroglial cells. Moreover, immunohistochemistry for several astroglial cells and polydendrocyte markers, both in the Nkx2.1-/- and control embryos and in the neurospheres, has revealed a severe loss of both glial cell types in the Nkx2.1 mutants. We found that the loss of glia corresponded to a decrease of Nkx2.1-derived precursor division capacity and glial differentiation. There was a drastic decrease of BrdU+ dividing cells labeled for Nkx2.1 in the MGE*, the POA* and the septal nucleus* of Nkx2.1 mutants. In addition, we noticed that while some remaining Nkx2.1+ precursors still succeeded to give rise to post-mitotic neurons in vitro and in vivo in the Nkx2.1-/-, they completely lost the capacity to differentiate in astrocytes. Altogether, these observations indicate for the first time that the transcription factor Nkx2.1 regulates the proliferation and differentiation of precursors in three subpallial domains that generate early embryonic astroglia and polydendrocytes. Furthermore, in order to investigate the potential function of these early Nkx2.1- derived glia, we have performed multiple immunohistochemical stainings on Nkx2.1-/- and wild-type animals, and Nkx2.1-Cre mice that were crossed to Rosa-DTA+/- mice in which the highly toxic diphtheria toxin aided to selectively deplete a majority of the Nkx2.1-derived cells. Interestingly, in these two mutants, we observed a drastic and significant loss of GFAP+, GLAST+, NG2+ and S100ß+ astroglial cells at the telencephalic midline and in the medial cortical areas. This cells loss could be directly correlated with severe axonal guidance defects observed in the corpus callosum (CC), the hippocampal commissure (HIC), the fornix (F) and the anterior commissure (AC). Axonal guidance is a key step allowing neurons to form specific connections and to become organized in a functional network. The contribution of guidepost cells inside the CC and the AC in mediating the growth of commissural axons have until now been attributed to specialized midline guidepost astroglia. Previous published results in our group have unravelled that, during embryonic development, the CC is populated in addition to astroglia by numerous glutamatergic and GABAergic guidepost neurons that are essential for the correct midline crossing of callosal axons. Therefore, the relative contribution of individual neuronal or glial populations towards the guidance of commissural axons remains largely to be investigated to understand guidance mechanisms further. Thus, we crossed Nkx2.1-Cre mice with NSE-DTA+/- mice that express the diphtheria toxin only in neurons and allowed us to selectively deplete Nkx2.1-derived GABAergic neurons. Interestingly, in the Nkx2.1-/- mice, the CC midline was totally disorganized and the callosal axons partly lost their orientation, whereas in the Nkx2.1Cre+/Rosa-DTA+/- and the Nkx2.1Cre+/NSE-DTA+/- mice, the axonal organization of the CC was not affected. In the three types of mice, hippocampal axons of the fornix were not properly fasciculated and formed disoriented bundles through the septum. Additionally, the AC formation was completely absent in Nkx2.1-/- mice and the AC was divided into two/three separate paths in the Nkx2.1Cre+/Rosa-DTA+/- mice that project in wrong territories. On the other hand, the AC didn't form or was reduced to a relatively narrower tract in the Nkx2.1Cre+/NSE-DTA+/- mice as compared to wild-type AC. These results clearly indicate that midline Nkx2.1-derived cells play a major role in commissural axons pathfinding and that both Nkx2.1-derived guidepost neurons and glia are necessary elements for the correct development of these commissures. Furthermore, during our investigations on Nkx2.1-/- and Nkx2.1Cre+/Rosa-DTA+/- mice, we noticed similar and severe defects in the erythrocytes distribution and the blood vessels network morphology in the embryonic brain of both mutants. As the Cre-mediated recombination was never observed to occur in the blood vessels of Nkx2.1-Cre mice, we inferred that the vessels defects observed were due to the loss of Nkx2.1-derived cells and not to the cells autonomous effects of Nkx2.1 in regulating endothelial cell precursors. Thereafter, the respective contribution of individual Nkx2.1-regulated neuronal or glial populations in the blood vessels network building were studied with the use of transgenic mice strains. Indeed, the use of Nkx2.1Cre+/NSE-DTA+/- mice indicated that the Nkx2.1-derived neurons were not implicated in this process. Finally, to discriminate between the two Nkx2.1-derived glial cell populations, the GLAST+ astroglia and the NG2+ polydendrocytes, an NG2-Cre mouse strain crossed to the Rosa-DTA+/- mice was used. In that mutant, the blood vessel network and the erythrocytes distribution were similarly affected as observed in Nkx2.1Cre+/Rosa-DTA+/- animals. Therefore, this result indicates that most probably, the NG2+ polydendrocytes are involved in helping to build the vessels network in the brain. Taken altogether, these observations show that during brain development, Nkx2.1- derived embryonic glial cells act as guidepost cells on the guidance of axons as well as forming vessels. Both Nkx2.1-regulated guidepost GABAergic neurons and glia collaborate to guide growing commissural axons, while polydendrocytes are implicated in regulating brain angiogenesis. - Le tissu cérébral est composé de cellules neuronales et gliales générées dans les couches germinales qui bordent les ventricules. Ces cellules se divisent, se différencient et migrent selon des voies particulières. La spécification des interneurones GABAergiques et des neurones glutamatergiques a été largement étudiée, par contre, l'origine, le destin et la fonction des cellules gliales précoces du télencéphale embryonnaire restent peu élucidées. Depuis longtemps, il était communément accepté que les cellules gliales, et plus particulièrement les astrocytes, sont générés après la neurogénèse à partir du télencéphale dorsal. Toutefois, notre travail montre que de nombreuses cellules gliales sont générées à partir de précurseurs ventraux qui expriment le gène Nkx2.1, entre E14.5 et E16.5, c'est-à dire,à des stades embryonnaires très précoces. Le gène NK2 homéobox 1 (Nkx2.1) appartient à une famille de facteurs de transcription appelée NK2. Il s'agit de protéines qui contiennent un homéo-domaine. La spécification des précurseurs de la MGE requiert l'expression du gène homéobox Nkx2.1. De plus, la fonction du gène Nkx2.1 dans la régulation de la spécification des interneurones GABAergiques et des oligodendrocytes dans le télencéphale ventral était déjà connue. Au cours de mon travail de thèse, j'ai également mis en évidence que, Nkx2.1 régule aussi les étapes de prolifération et de différenciation de divers sous-types de cellules gliales soit de type astrocytes ou bien polydendrocytes. L'utilisation d'un anticorps contre la protéine Nkx2.1 ainsi qu'une sonde à ribonucléotides contre l'ARN messager du gène Nkx2.1 ont révélé la présence de nombreuses cellules positives pour Nkx2.1 qui exprimaient des marqueurs astrocytaires (comme GLAST et GFAP) dans le télencéphale embryonnaire. Afin de déterminer de manière sélective le sort des interneurones GABAergiques, des polydendrocytes et des astrocytes dérivés de la MGE, nous avons croisé soit des souris Nkx2.1-Cre, des souris Glast-Cre ERT+/- inductibles ou bien des souris NG2-Cre avec des souris Rosa26-lox-STOP-lox-YFP (Rosa26-YFP) Cre rapportrices. L'origine précise des astroglies positives pour Nkx2.1 a été directement établie en combinant une coloration immunologique pour les glies et une électroporation focale d'un plasmide pCAG-GS-EGFP dans les domaines subpalliaux de tranches organotypiques, puis également, par des cultures de neurosphères in vitro et des expériences d'électroporation in utero d'un plasmide pCAG-GS-tomato dans le pallium ventral d'embryons Nkx2.1-Cre+/Rosa- YFP+/- au stade E14.5. Nous avons donc confirmé que les trois régions germinales du télencéphale ventral, c'est-à-dire, la MGE, l'AEP/POA et le noyau triangulaire septal sont capables de générer des cellules astrogliales. D'autre part, l'immunohistochimie pour plusieurs marqueurs d'astrocytes ou de polydendrocytes, dans les embryons Nkx2.1-/- et contrôles ainsi que dans les neurosphères, a révélé une sévère perte de ces deux types gliaux chez les mutants. Nous avons trouvé que la perte de glies correspondait à une diminution de la capacité de division des précurseurs dérivés de Nkx2.1, ainsi que l'incapacité de ces précurseurs de se différencier en cellules gliales. Nous avons en effet observé une diminution importante des cellules BrdU+ en division exprimant Nkx2.1dans la MGE*, la POA* et le noyau septal* des mutants pour Nkx2.1. D'autre part, nous avons pu mettre en évidence aussi bien in vitro, qu'in vivo, que certains précurseurs Nkx2.1+ chez le mutant gardent la capacité à se différencier en neurones tandis qu'ils perdent celle de se différencier en cellules gliales. Prises dans leur ensemble, ces observations indiquent pour la première fois que le facteur de transcription Nkx2.1 régule les étapes de prolifération et de différentiation des précurseurs des trois domaines subpalliaux qui génèrent les astroglies et polydendrocytes embryonnaires précoces. Par la suite, dans le but de comprendre la fonction potentielle de ces glies précoces, nous avons procédé à de multiples colorations immunohistochimiques sur des animaux Nkx2.1-/- et sauvages, ainsi que sur des souris Nkx2.1-Cre croisées à des souris Rosa-DTA+/- dans lesquelles la toxine diphthérique hautement toxique a permis de supprimer sélectivement la majorité des cellules dérivées de Nkx2.1. De manière intéressante, nous avons observé dans ces deux mutants, une perte drastique et significative de cellules astrogliales GFAP+, GLAST+ et polydendrocytaires NG2+ et S100ß+ dans le télencéphale, à la midline et dans les aires corticales médianes. Ces pertes ont pu être directement corrélées avec des défauts de guidage axonal observés dans le corps calleux (CC), la commissure hippocampique (HIC), le fornix (F) et la commissure antérieure (AC). Le guidage axonal est une étape clé permettant aux neurones de former des connections spécifiques et de s'organiser dans un réseau fonctionnel. La contribution des cellules « guidepost » dans le CC et dans la AC comme médiateurs de la croissance des axones commissuraux à jusqu'à aujourd'hui été attribuée spécifiquement à des astroglies « guidepost » de la midline. Des résultats publiés précédemment dans notre groupe, ont permis de montrer que, pendant le développement embryonnaire, le CC est peuplé en plus de la glie par de nombreux neurones « guidepost » glutamatergiques et GABAergiques qui sont essentiels pour le croisement correct des axones callosaux à la midline. Ainsi, la contribution relative des populations individuelles neuronales ou gliales pour le guidage des axones commissuraux demande à être approfondie afin de mieux comprendre les mécanismes de guidage. A ces fins, nous avons croisé des souris Nkx2.1-Cre avec des souris NSE-DTA+/- qui expriment la toxine diphthérique uniquement dans les neurones et ainsi, nous avons pu sélectivement supprimer les neurones dérivés de domaines Nkx2.1+. Dans les souris Nkx2.1-/-,nous avons découvert que le CC était désorganisé avec des axones callosaux perdant partiellement leur orientation, alors que dans les souris Nkx2.1Cre+/Rosa-DTA+/- et Nkx2.1Cre+/NSE-DTA+/-, l'organisation axonale n'était pas affectée. De plus, les faisceaux hippocampiques du fornix étaient défasciculés dans les trois types de mutants. Par ailleurs, la formation de la commissure antérieure (AC) était complètement absente dans les souris Nkx2.1-/- d'une part, et d'autre part, celle-ci était divisée en deux à trois voies séparées dans les souris Nkx2.1Cre+/Rosa-DTA+/-. Finalement, la AC était soit absente, soit réduite de manière ne former plus qu'un faisceau relativement plus étroit dans les souris Nkx2.1Cre+/NSE-DTA+/- en comparaison avec la AC sauvage. Ces derniers résultats indiquent clairement que les cellules dérivées de Nkx2.1 à la midline, jouent un rôle majeur dans le guidage des axones commissuraux et que, autant les neurones, que les astrocytes « guidepost » dérivés de Nkx2.1, sont des éléments nécessaires au développement correct de ces commissures. En outre, lors de nos investigations sur les souris Nkx2.1-/- et Nkx2.1Cre+/Rosa-DTA+/-, nous avons remarqués des défauts sévères et similaires dans la distribution des erythrocytes et dans la morphologie du réseau de vaisseaux sanguins dans le cerveau embryonnaire des deux mutants précités. Puisque nous n'avons jamais observé de recombinaison de la Cre recombinase dans les vaisseaux sanguins des souris Nkx2.1Cre, nous en avons déduit que les défauts de vaisseaux observés étaient dus à la perte de cellules dérivées de Nkx2.1. Il existerait donc en plus de la fonction cellulaire autonome de Nkx2.1 reconnue pour régulée directement la spécification des cellules endothéliales, une fonction indirecte de Nkx2.1. Afin de déterminer la contribution respective des populations individuelles neuronales ou gliales régulées par Nkx2.1 dans la construction du réseau de vaisseaux sanguins, nous avons utilisé diverses lignées de souris transgéniques. L'utilisation de souris Nkx2.1Cre+/NSE-DTA+/- a indiqué que les neurones dérivés de Nkx2.1 n'étaient pas impliqués dans ce processus. Finalement, afin de discriminer entre les deux populations de cellules gliales dérivées de Nkx2.1, les astroglies et les polydendrocytes, nous avons croisé une lignée de souris NG2-Cre avec des souris Rosa-DTA+/-. Dans ce dernier mutant, le réseau de vaisseaux sanguins du cortex ainsi que la distribution des erythrocytes étaient affectés de la même manière que dans le cortex des souris Nkx2.1Cre+/Rosa-DTA+/-. Par conséquent, ce résultat indique que très probablement, les polydendrocytes NG2+ sont impliqués dans la mise en place du réseau de vaisseaux dans le cerveau. Prises dans leur ensemble, ces observations montrent que durant le développement embryonnaire du cerveau, des sous-populations de glies régulées par Nkx2.1 jouent un rôle de cellules « guidepost » dans le guidage des axones, ainsi que des vaisseaux. Les polydendrocytes sont impliquées dans la régulation de l'angiogenèse tandis que, autant les neurones GABAergiques que les astrocytes collaborent dans le guidage des axones commissuraux en croissance.

Tree-based message diffusion for managing replicated data in unreliable and resource-constrained peer-to-peer environment

Abstract This thesis proposes a set of adaptive broadcast solutions and an adaptive data replication solution to support the deployment of P2P applications. P2P applications are an emerging type of distributed applications that are running on top of P2P networks. Typical P2P applications are video streaming, file sharing, etc. While interesting because they are fully distributed, P2P applications suffer from several deployment problems, due to the nature of the environment on which they perform. Indeed, defining an application on top of a P2P network often means defining an application where peers contribute resources in exchange for their ability to use the P2P application. For example, in P2P file sharing application, while the user is downloading some file, the P2P application is in parallel serving that file to other users. Such peers could have limited hardware resources, e.g., CPU, bandwidth and memory or the end-user could decide to limit the resources it dedicates to the P2P application a priori. In addition, a P2P network is typically emerged into an unreliable environment, where communication links and processes are subject to message losses and crashes, respectively. To support P2P applications, this thesis proposes a set of services that address some underlying constraints related to the nature of P2P networks. The proposed services include a set of adaptive broadcast solutions and an adaptive data replication solution that can be used as the basis of several P2P applications. Our data replication solution permits to increase availability and to reduce the communication overhead. The broadcast solutions aim, at providing a communication substrate encapsulating one of the key communication paradigms used by P2P applications: broadcast. Our broadcast solutions typically aim at offering reliability and scalability to some upper layer, be it an end-to-end P2P application or another system-level layer, such as a data replication layer. Our contributions are organized in a protocol stack made of three layers. In each layer, we propose a set of adaptive protocols that address specific constraints imposed by the environment. Each protocol is evaluated through a set of simulations. The adaptiveness aspect of our solutions relies on the fact that they take into account the constraints of the underlying system in a proactive manner. To model these constraints, we define an environment approximation algorithm allowing us to obtain an approximated view about the system or part of it. This approximated view includes the topology and the components reliability expressed in probabilistic terms. To adapt to the underlying system constraints, the proposed broadcast solutions route messages through tree overlays permitting to maximize the broadcast reliability. Here, the broadcast reliability is expressed as a function of the selected paths reliability and of the use of available resources. These resources are modeled in terms of quotas of messages translating the receiving and sending capacities at each node. To allow a deployment in a large-scale system, we take into account the available memory at processes by limiting the view they have to maintain about the system. Using this partial view, we propose three scalable broadcast algorithms, which are based on a propagation overlay that tends to the global tree overlay and adapts to some constraints of the underlying system. At a higher level, this thesis also proposes a data replication solution that is adaptive both in terms of replica placement and in terms of request routing. At the routing level, this solution takes the unreliability of the environment into account, in order to maximize reliable delivery of requests. At the replica placement level, the dynamically changing origin and frequency of read/write requests are analyzed, in order to define a set of replica that minimizes communication cost.

Ab initio benchmark study for the oxidative addition of CH4 to Pd: importance of basis-set flexibility and polarization

To obtain a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the methane C-H bond to the palladium atom, we have explored this PES using a hierarchical series of ab initio methods (Hartree-Fock, second-order Møller-Plesset perturbation theory, fourth-order Møller-Plesset perturbation theory with single, double and quadruple excitations, coupled cluster theory with single and double excitations (CCSD), and with triple excitations treated perturbatively [CCSD(T)]) and hybrid density functional theory using the B3LYP functional, in combination with a hierarchical series of ten Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Counterpoise corrected relative energies of stationary points are converged to within 0.1-0.2 kcal/mol as a function of the basis-set size. Our best estimate of kinetic and thermodynamic parameters is -8.1 (-8.3) kcal/mol for the formation of the reactant complex, 5.8 (3.1) kcal/mol for the activation energy relative to the separate reactants, and 0.8 (-1.2) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). This agrees well with available experimental data. Our work highlights the importance of sufficient higher angular momentum polarization functions, f and g, for correctly describing metal-d-electron correlation and, thus, for obtaining reliable relative energies. We show that standard basis sets, such as LANL2DZ+ 1f for palladium, are not sufficiently polarized for this purpose and lead to erroneous CCSD(T) results. B3LYP is associated with smaller basis set superposition errors and shows faster convergence with basis-set size but yields relative energies (in particular, a reaction barrier) that are ca. 3.5 kcal/mol higher than the corresponding CCSD(T) values

High cefepime plasma concentrations and neurological toxicity in febrile neutropenic patients with mild impairment of renal function.

High-dose cefepime therapy is recommended for febrile neutropenia. Safety issues have been raised in a recent meta-analysis reporting an increased risk of mortality during cefepime therapy. Cefepime-related neurological toxicity has been associated with overdosing due to severe renal dysfunction. This study aimed to investigate the association between cefepime plasma concentrations and neurological toxicity in febrile neutropenic patients. Cefepime trough concentrations (by high-performance liquid chromatography) were retrospectively analyzed for 30 adult febrile neutropenic patients receiving the recommended high-dose regimen (6 g/day for a glomerular filtration rate [GFR] of >50 ml/min). The dose adjustment to renal function was evaluated by the ratio of the cefepime daily dose per 100 ml/min of glomerular filtration. The association between cefepime plasma concentrations and neurological toxicity was assessed on the basis of consistent neurological symptoms and/or signs (by NCI criteria). The median cefepime concentration was 8.7 mg/liter (range, 2.1 to 38 mg/liter) at a median of 4 days (range, 2 to 15 days) after the start of therapy. Neurological toxicity (altered mental status, hallucinations, or myoclonia) was attributed to cefepime in 6/30 (20%) patients (median GFR, 45 ml/min; range, 41 to 65 ml/min) receiving a median dose of 13.2 g/day per 100 ml/min GFR (range, 9.2 to 14.3 g/day per 100 ml/min GFR). Cefepime discontinuation resulted in complete neurological recovery for five patients and improvement for one patient. A multivariate logistic regression model confirmed high cefepime concentrations as an independent predictor of neurological toxicity, with a 50% probability threshold at ≥22 mg/liter (P = 0.05). High cefepime plasma concentrations are associated with neurological toxicity in febrile neutropenic patients with mild renal dysfunction. Careful adherence to normalized dosing per 100 ml/min GFR is crucial. Monitoring of plasma concentrations may contribute to preventing neurological toxicity of high-dose therapy for this life-threatening condition.

THE ROLE OF SPINDLES FOR SLEEP: MANIPULATING OSCILLATORY ACTIVITY IN THE THALAMOCORTICAL NETWORK

Modern urban lifestyle encourages the prolongation of wakefulness, leaving less and less time for sleep. Although the exact functions of sleep remain one of the biggest mysteries in neuroscience, the society is well aware of the negative consequences of sleep loss on human physical and mental health and performance. Enhancing sleep's recuperative functions might allow shortening sleep duration while preserving the beneficial effects of sleep. During sleep, brain activity oscillates across a continuum of frequencies. Individual oscillations have been suggested to underlie distinct functions for sleep and cognition. Gaining control about individual oscillations might allow boosting their specific functions. Sleep spindles are 11 - 15 Hz oscillations characteristic for light non-rapid-eye-movement sleep (NREMS) and have been proposed to play a role in memory consolidation and sleep protection against environmental stimuli. The reticular thalamic nucleus (nRt) has been identified as the major pacemaker of spindles. Intrinsic oscillatory burst discharge in nRt neurons, arising from the interplay of low-threshold (T-type) Ca2+ channels (T channels) and small conductance type 2 (SK2) K+ channels (SK2 channels), underlies this pacemaking function. In the present work we investigated the impact of altered nRt bursting on spindle generation during sleep by studying mutant mice for SK2 channels and for CaV3.3 channels, a subtype of T channels. Using in vitro electrophysiology I showed that nRt bursting was abolished in CaV3.3 knock out (CaV3.3 KO) mice. In contrast, in SK2 channel over-expressing (SK2-OE) nRt cells, intrinsic repetitive bursting was prolonged. Compared to wildtype (WT) littermates, altered nRt burst discharge lead to weakened thalamic network oscillations in vitro in CaV3.3 KO mice, while oscillatory activity was prolonged in SK2-OE mice. Sleep electroencephalographic recordings in CaV3.3 KO and SK2-OE mice revealed that reduced or potentiated nRt bursting respectively weakened or prolonged sleep spindle activity at the NREMS - REMS transition. Furthermore, SK2-OE mice showed more consolidated NREMS and increased arousal thresholds, two correlates of good sleep quality. This thesis work suggests that CaV3.3 and SK2 channels may be targeted in order to modulate sleep spindle activity. Furthermore, it proposes a novel function for spindles in NREMS consolidation. Finally, it provides evidence that sleep quality may be improved by promoting spindle activity, thereby supporting the hypothesis that sleep quality can be enhanced by modulating oscillatory activity in the brain. Le style de vie moderne favorise la prolongation de l'éveil, laissant de moins en moins de temps pour le sommeil. Même si le rôle exact du sommeil reste un des plus grands mystères des neurosciences, la société est bien consciente des conséquences négatives que provoque un manque de sommeil, à la fois sur le plan de la santé physique et mentale ainsi qu'au niveau des performances cognitives. Augmenter les fonctions récupératrices du sommeil pourrait permettre de raccourcir la durée du sommeil tout en en conservant les effets bénéfiques. Durant le sommeil, on observe des oscillations à travers un continuum de fréquences. Il a été proposé que chaque oscillation pourrait être à l'origine de fonctions spécifiques pour le sommeil et la cognition. Pouvoir de contrôler les oscillations individuelles permettrait d'augmenter leurs fonctions respectives. Les fuseaux sont des oscillations de 11 à 15 Hz caractéristiques du sommeil à ondes lentes léger et il a été suggéré qu'elles jouent un rôle majeur pour la consolidation de la mémoire ainsi que dans la protection du sommeil contre les stimuli environnementaux. Le nucleus réticulaire du thalamus (nRt) a été identifié en tant que générateur de rythme des fuseaux. Les bouffées oscillatoires intrinsèques des neurones du nRt, provenant de l'interaction de canaux calciques à bas seuil de type T (canaux T) et de canaux potassiques à faible conductance de type 2 (canaux SK2), sont à l'origine de la fonction de générateur de rythme. Dans ce travail, j'ai étudié l'impact de la modulation de bouffées de nRT sur la génération des fuseaux pendant le sommeil en investiguant des souris génétiquement modifiées pour les canaux SK2 et les canaux CaV3.3, un sous-type de canaux T. En utilisant l'électrophysiologie in vitro j'ai démontré que les bouffées du nRT étaient abolies dans les souris knock-out du type CaV3.3 (CaV3.3 KO). D'autre part, dans les cellules nRT sur-exprimant les canaux SK2 (SK2-OE), les bouffées oscillatoires intrinsèques étaient prolongées. Par rapport aux souris wild type, les souris CaV3.3 KO ont montré un affaiblissement des oscillations thalamiques en réponse à un changement des bouffées de nRT, alors que l'activité oscillatoire était prolongée dans les souris SK2-OE. Des enregistrements EEG du sommeil dans des souris de type CaV3.3 KO et SK2-OE ont révélé qu'une réduction ou augmentation des bouffées nRT ont respectivement affaibli ou prolongé l'activité des fuseaux durant les transitions du sommeil à ondes lentes au sommeil paradoxal. De plus, les souris SK2-OE ont montré des signes de consolidation du sommeil à ondes lentes et un seuil augmenté pour le réveil, deux mesures qui corrèlent avec une bonne qualité du sommeil. Le travail de cette thèse propose que les canaux CaV3.3 et SK2 pourrait être ciblés pour moduler l'activité des fuseaux. De plus, je propose une fonction nouvelle pour les fuseaux dans la consolidation du sommeil à ondes lentes. Finalement je suggère que la qualité du sommeil peut être améliorée en promouvant l'activité des fuseaux, soutenant ainsi l'idée que la qualité du sommeil peut être améliorée en modulant l'activité oscillatoire dans le cerveau.

A regulatory network for coordinated flower maturation.

For self-pollinating plants to reproduce, male and female organ development must be coordinated as flowers mature. The Arabidopsis transcription factors AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8 regulate this complex process by promoting petal expansion, stamen filament elongation, anther dehiscence, and gynoecium maturation, thereby ensuring that pollen released from the anthers is deposited on the stigma of a receptive gynoecium. ARF6 and ARF8 induce jasmonate production, which in turn triggers expression of MYB21 and MYB24, encoding R2R3 MYB transcription factors that promote petal and stamen growth. To understand the dynamics of this flower maturation regulatory network, we have characterized morphological, chemical, and global gene expression phenotypes of arf, myb, and jasmonate pathway mutant flowers. We found that MYB21 and MYB24 promoted not only petal and stamen development but also gynoecium growth. As well as regulating reproductive competence, both the ARF and MYB factors promoted nectary development or function and volatile sesquiterpene production, which may attract insect pollinators and/or repel pathogens. Mutants lacking jasmonate synthesis or response had decreased MYB21 expression and stamen and petal growth at the stage when flowers normally open, but had increased MYB21 expression in petals of older flowers, resulting in renewed and persistent petal expansion at later stages. Both auxin response and jasmonate synthesis promoted positive feedbacks that may ensure rapid petal and stamen growth as flowers open. MYB21 also fed back negatively on expression of jasmonate biosynthesis pathway genes to decrease flower jasmonate level, which correlated with termination of growth after flowers have opened. These dynamic feedbacks may promote timely, coordinated, and transient growth of flower organs.

Towards robust network based complex systems : from evolutionary cellular automata to biological models

Abstract Sitting between your past and your future doesn't mean you are in the present. Dakota Skye Complex systems science is an interdisciplinary field grouping under the same umbrella dynamical phenomena from social, natural or mathematical sciences. The emergence of a higher order organization or behavior, transcending that expected of the linear addition of the parts, is a key factor shared by all these systems. Most complex systems can be modeled as networks that represent the interactions amongst the system's components. In addition to the actual nature of the part's interactions, the intrinsic topological structure of underlying network is believed to play a crucial role in the remarkable emergent behaviors exhibited by the systems. Moreover, the topology is also a key a factor to explain the extraordinary flexibility and resilience to perturbations when applied to transmission and diffusion phenomena. In this work, we study the effect of different network structures on the performance and on the fault tolerance of systems in two different contexts. In the first part, we study cellular automata, which are a simple paradigm for distributed computation. Cellular automata are made of basic Boolean computational units, the cells; relying on simple rules and information from- the surrounding cells to perform a global task. The limited visibility of the cells can be modeled as a network, where interactions amongst cells are governed by an underlying structure, usually a regular one. In order to increase the performance of cellular automata, we chose to change its topology. We applied computational principles inspired by Darwinian evolution, called evolutionary algorithms, to alter the system's topological structure starting from either a regular or a random one. The outcome is remarkable, as the resulting topologies find themselves sharing properties of both regular and random network, and display similitudes Watts-Strogtz's small-world network found in social systems. Moreover, the performance and tolerance to probabilistic faults of our small-world like cellular automata surpasses that of regular ones. In the second part, we use the context of biological genetic regulatory networks and, in particular, Kauffman's random Boolean networks model. In some ways, this model is close to cellular automata, although is not expected to perform any task. Instead, it simulates the time-evolution of genetic regulation within living organisms under strict conditions. The original model, though very attractive by it's simplicity, suffered from important shortcomings unveiled by the recent advances in genetics and biology. We propose to use these new discoveries to improve the original model. Firstly, we have used artificial topologies believed to be closer to that of gene regulatory networks. We have also studied actual biological organisms, and used parts of their genetic regulatory networks in our models. Secondly, we have addressed the improbable full synchronicity of the event taking place on. Boolean networks and proposed a more biologically plausible cascading scheme. Finally, we tackled the actual Boolean functions of the model, i.e. the specifics of how genes activate according to the activity of upstream genes, and presented a new update function that takes into account the actual promoting and repressing effects of one gene on another. Our improved models demonstrate the expected, biologically sound, behavior of previous GRN model, yet with superior resistance to perturbations. We believe they are one step closer to the biological reality.

A new compact linear programming formulation for choice network revenue management

The choice network revenue management model incorporates customer purchase behavioras a function of the offered products, and is the appropriate model for airline and hotel networkrevenue management, dynamic sales of bundles, and dynamic assortment optimization.The optimization problem is a stochastic dynamic program and is intractable. A certainty-equivalencerelaxation of the dynamic program, called the choice deterministic linear program(CDLP) is usually used to generate dyamic controls. Recently, a compact linear programmingformulation of this linear program was given for the multi-segment multinomial-logit (MNL)model of customer choice with non-overlapping consideration sets. Our objective is to obtaina tighter bound than this formulation while retaining the appealing properties of a compactlinear programming representation. To this end, it is natural to consider the affine relaxationof the dynamic program. We first show that the affine relaxation is NP-complete even for asingle-segment MNL model. Nevertheless, by analyzing the affine relaxation we derive a newcompact linear program that approximates the dynamic programming value function betterthan CDLP, provably between the CDLP value and the affine relaxation, and often comingclose to the latter in our numerical experiments. When the segment consideration sets overlap,we show that some strong equalities called product cuts developed for the CDLP remain validfor our new formulation. Finally we perform extensive numerical comparisons on the variousbounds to evaluate their performance.

Molecular basis of odor detection in insects.

Olfactory systems are evolutionarily ancient, underlying the common requirement for all animals to sense and respond to diverse volatile chemical signals in their environment. Odor detection is mediated by odorant receptors (ORs) that, in most olfactory systems, comprise large families of divergent G protein-coupled receptors. Here, I discuss our and others' recent investigations of ORs in the fruit fly, Drosophila melanogaster, which have revealed insights into the distinct evolutionary origin and molecular function of insect ORs. I also describe a bioinformatics strategy that we developed to identify molecules that function with these insect-specific receptors in odor detection.

The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review).

During the last 2 years, several novel genes that encode glucose transporter-like proteins have been identified and characterized. Because of their sequence similarity with GLUT1, these genes appear to belong to the family of solute carriers 2A (SLC2A, protein symbol GLUT). Sequence comparisons of all 13 family members allow the definition of characteristic sugar/polyol transporter signatures: (1) the presence of 12 membrane-spanning helices, (2) seven conserved glycine residues in the helices, (3) several basic and acidic residues at the intracellular surface of the proteins, (4) two conserved tryptophan residues, and (5) two conserved tyrosine residues. On the basis of sequence similarities and characteristic elements, the extended GLUT family can be divided into three subfamilies, namely class I (the previously known glucose transporters GLUT1-4), class II (the previously known fructose transporter GLUT5, the GLUT7, GLUT9 and GLUT11), and class III (GLUT6, 8, 10, 12, and the myo-inositol transporter HMIT1). Functional characteristics have been reported for some of the novel GLUTs. Like GLUT1-4, they exhibit a tissue/cell-specific expression (GLUT6, leukocytes, brain; GLUT8, testis, blastocysts, brain, muscle, adipocytes; GLUT9, liver, kidney; GLUT10, liver, pancreas; GLUT11, heart, skeletal muscle). GLUT6 and GLUT8 appear to be regulated by sub-cellular redistribution, because they are targeted to intra-cellular compartments by dileucine motifs in a dynamin dependent manner. Sugar transport has been reported for GLUT6, 8, and 11; HMIT1 has been shown to be a H+/myo-inositol co-transporter. Thus, the members of the extended GLUT family exhibit a surprisingly diverse substrate specificity, and the definition of sequence elements determining this substrate specificity will require a full functional characterization of all members.

The Oncoprotein BCL11A Binds to Orphan Nuclear Receptor TLX and Potentiates its Transrepressive Function

Nuclear orphan receptor TLX (NR2E1) functions primarily as a transcriptional repressor and its pivotal role in brain development, glioblastoma, mental retardation and retinopathologies make it an attractive drug target. TLX is expressed in the neural stem cells (NSCs) of the subventricular zone and the hippocampus subgranular zone, regions with persistent neurogenesis in the adult brain, and functions as an essential regulator of NSCs maintenance and self-renewal. Little is known about the TLX social network of interactors and only few TLX coregulators are described. To identify and characterize novel TLX-binders and possible coregulators, we performed yeast-two-hybrid (Y2H) screens of a human adult brain cDNA library using different TLX constructs as baits. Our screens identified multiple clones of Atrophin-1 (ATN1), a previously described TLX interactor. In addition, we identified an interaction with the oncoprotein and zinc finger transcription factor BCL11A (CTIP1/Evi9), a key player in the hematopoietic system and in major blood-related malignancies. This interaction was validated by expression and coimmunoprecipitation in human cells. BCL11A potentiated the transrepressive function of TLX in an in vitro reporter gene assay. Our work suggests that BCL11A is a novel TLX coregulator that might be involved in TLX-dependent gene regulation in the brain.

Expression and function of the NALP3 inflammasome in rheumatoid synovium.

Summary The NACHT, LRR and PYD domains containing protein (NALP3) inflammasome is a key regulator of interleukin-1beta (IL-1beta) secretion. As there is strong evidence for a pro-inflammatory role of IL-1beta in rheumatoid arthritis (RA) and in murine models of arthritis, we explored the expression of the different components of the NALP3 inflammasome as well as other nucleotide oligomerization domain (NOD)-like receptors (NLRs) in synovium obtained from patients with RA. The expression of NLRs was also studied in fibroblast lines derived from joint tissue. By immunohistology, NALP3 and apoptosis-associated speck-like protein containing a CARD domain (ASC) were expressed in myeloid and endothelial cells and B cells. T cells expressed ASC but lacked NALP3. In synovial fibroblast lines, NALP3 expression was not detected at the RNA and protein levels and stimulation with known NALP3 agonists failed to induce IL-1beta secretion. Interestingly, we were unable to distinguish RA from osteoarthritis synovial samples on the basis of their basal level of RNA expression of known NLR proteins, though RA samples contained higher levels of caspase-1 assayed by enzyme-linked immunsorbent assay. These results indicate that myeloid and endothelial cells are the principal sources of inflammasome-mediated IL-1beta production in the synovium, and that synovial fibroblasts are unable to activate caspase-1 because they lack NALP3. The NALP3 inflammasome activity does not account for the difference in level of inflammation between RA and osteoarthritis.

The role of the transcription factor Tcf-1 for the development and the function of NK cells

Natural Killer (NK) cells are innate immune cells that can eliminate malignant and foreign cells and that play an important role for the early control of viral and fungal infections. Further, they are important regulators of the adaptive and innate immune responses. During their development in the bone marrow (BM) NK cells undergo several maturation steps that directly establish an effector program. The transcriptional network that controls NK cell development and maturation is still incompletely understood. Based on earlier findings that NK cell numbers are reduced in the absence of the transcription factor T cell factor-1 (Tcf-1), my thesis has addressed the precise role of this transcription factor for NK cell development, maturation and function and whether Tcf-1 acts as a nuclear effector of the canonical Wnt signaling pathway to mediate its effects. It is shown that Tcf-1 is selectively required for the emergence of mature BM NK cells. Surprisingly, the emergence of BM NK cells depends on the repressor function of Tcf-1 and is independent of the Wnt pathway. In BM and peripheral NK cells Tcf-1 is found to suppress Granzyme B (GzmB) expression, a key cytotoxic effector molecule required to kill target cells. We provide evidence that GzmB over-expression in the absence of Tcf-1 results in accelerated spontaneous death of bone marrow NK cells and of cytokine stimulated peripheral NK cells. Moreover, Tcf-1 deficient NK cells show reduced target cell killing, which is due to enhanced GzmB-dependent NK cell death induced by the recognition of tumour target cells. Collectively, these data provide significant new insights into the transcriptional regulation of NK cell development and function and suggest a novel mechanism that protects NK cells from the deleterious effects of highly cytotoxic effector molecules. - Les cellules NK (de l'anglais Natural Killer) font partie du système immunitaire inné et sont capables d'éliminer à elles seules les cellules cancéreuses ou infectées. Ces cellules participent dans la régulation et la coordination des réponses innée et adaptative. Lors de leur développement dans la moelle osseuse, les cellules NK vont acquérir leurs fonctions effectrices, un processus contrôlé par des facteurs de transcription mais encore peu connu. Des précédentes travaux ont montré qu'une diminution du nombre de cellules NK corrélait avec l'absence du facteur de transcription Tcf-1 (T cell factor-1), suggérant un rôle important de Tcf-1 dans le développement de cellules NK. Cette thèse a pour but de mieux comprendre le rôle du facteur de transcription Tcf-1 lors du développement et la maturation des cellules NK, ainsi que son interaction avec la voie de signalisation Wnt. Nous avons montré que Tcf-1 est essentiel pour la transition des cellules immatures NK (iNK) à des cellules matures NK (mNK) dans la moelle osseuse, et cela de manière indépendamment de la voie de signalisation Wnt. De manière intéressante, nous avons observé qu'en absence du facteur de transcription Tcf-1, les cellules NK augmentaient l'expression de la protéine Granzyme B (GzmB), une protéine essentielle pour l'élimination des cellules cancéreuses ou infectées. Ceci a pour conséquence, une augmentation de la mort des cellules mNK dans la moelle osseuse ainsi qu'une diminution de leur fonction «tueuses». Ces résultats montrent pour la première fois, le rôle répresseur du facteur de transcription Tcf-1 dans l'expression de la protéine GzmB. L'ensemble de ces résultats apporte de nouveaux éléments concernant le rôle de Tcf-1 dans la régulation du développement et de la fonction des cellules NK et suggèrent un nouveau mécanisme cellulaire de protection contre les effets délétères d'une dérégulation de l'expression des molécules cytotoxique.

Flow cytofluorometric analysis of the binding of Vicia villosa lectin to T lymphoblasts: lack of correlation with cytolytic function.

The relationship between the binding of Vicia villosa (VV) lectin and the expression of cytolytic function in T lymphoblasts has been investigated using flow cytofluorometric techniques. Spleen cells activated in vitro in 5-day mixed leukocyte cultures (MLC) were incubated sequentially with VV, rabbit anti-V antiserum, and fluoresceinated sheep anti-rabbit IgG. When these stained MLC cells were passed on a flow cytometer gated to exclude nonviable cells and small lymphocytes, a single heterogeneous peak of fluorescence was seen, as compared to control MLC cells that had not been incubated with VV. Fluorescence of lymphoblasts was dependent upon lectin dose and was eliminated when staining was performed in the presence of N-acetyl-D-galactosamine, the appropriate competitive sugar for VV. T cell blast populations activated against H-2, Mls, or parasite antigens all had comparable levels of fluorescence after staining with VV, although the cytolytic activity of these cells varied widely. Furthermore, when MLC lymphoblasts binding large or small amounts of VV were sorted on the basis of their relative fluorescence intensity and tested for cytolytic function, no appreciable difference in activity between the 2 populations was observed. These results are inconsistent with the hypothesis that VV binds selectively to cytolytic T lymphocytes.