The COP9 SIGNALOSOME is required for postembryonic meristem maintenance in Arabidopsis thaliana

Cullin-RING E3 ligases (CRLs) regulate different aspects of plant development, and are activated by modification of their cullin subunit with the ubiquitin-like protein NEDD8 (NEural precursor cell expressed Developmentally Down-regulated 8) (neddylation) and deactivated by NEDD8 removal (deneddylation). The CONSTITUTIVELY PHOTOMORPHOGENIC9 (COP9) signalosome (CSN) acts as a molecular switch of CRLs activity by reverting their neddylation status, but its contribution to embryonic and early seedling development remains poorly characterized. Here, we analyzed the phenotypic defects of csn mutants and monitored the cullin deneddylation/neddylation ratio during embryonic and early seedling development. We show that while csn mutants can complete embryogenesis (albeit at a slower pace than wild type) and are able to germinate (albeit at a reduced rate), they progressively loose meristem activity upon germination, until they become unable to sustain growth. We also show that the majority of cullin proteins is progressively neddylated during the late stages of seed maturation and becomes deneddylated upon seed germination. This developmentally regulated shift in the cullin neddylation status is absent in csn mutants. We conclude that the CSN and its cullin deneddylation activity are required to sustain postembryonic meristem function in Arabidopsis

Cytotoxic T lymphocyte specificities during the acute and memory responses to lymphocytic choriomeningitis virus infection : ‡b a dissertation

The focus of experiments presented in this dissertation is to determine how signals created by exposure to environmental stimuli are integrated at the level of transcription, resulting in the generation of specific patterns of gene expression. The model system used was expression of the neurotensinl neuromedin N (NT/N) neuropeptide gene in the neuroendocrine PC12 cell line. This gene is synergistically activated in PC12 cells in response to nerve growth factor, lithium, glucocorticoids, and activators of adenylate cyclase. Several cis-regulatory elements were identified within a 200 bp regulatory region, including AP-1, CRE, and GRE-like elements. Mutational analysis confirmed the importance of these elements for responses to inducer combinations. The primary objective was to identify proteins that interact with NT/N promoter sequences and determine if they are important in mediating responses to inducer combinations. The first set of experiments was designed to investigate changes in AP-1 binding activity. Previous analysis had shown that mutation of the AP-1 site severely curtails responses to all inducer combinations indicating that AP-1 plays a pivotal role in NT/N gene activation. DNA binding studies using in vitro synthesized AP-1 proteins revealed that all heterodimeric combinations could bind both the AP-1 and JARE sites; however, these complexes displayed a higher affinity for the AP-1 site. c-Jun homodimers were also found to bind both these sites albeit with a lower affinity and with a preference for the JARE site. These studies revealed that specificity is probably not at the level of DNA binding. Therefore, it was possible that only a subset of AP-1 proteins were activated upon stimulation. DNase I footprint analysis using nuclear extracts from PC12 cells showed changes in protection at the consensus AP-1 site upon treatment with inducers suggesting changes in AP-1 binding activity. It was found that AP-1 binding activity was increased upon stimulation, with the major component being Jun B. However, substantial levels of c-Fos and c-Jun were also detected at some time points. These results coupled with transfection data demonstrating that forced expression of c-Jun and c-Fos result in potent synergistic activation of the NT/N promoter support the hypothesis that c-Jun and c-Fos are also involved in NT/N gene activation. DNase I footprinting studies using PC12 nuclear extracts also revealed substantial areas of protection surrounding the CRE element. This result, along with the high degree of conservation of these sequences between human and rat, suggested they play a role in the regulation of the NT/N gene in PC12 cells. Mutational analysis of this region showed that sequences upstream of the CRE were important for full activation of the NT/N promoter. Specific mutation of the CRE resulted in a 75% decrease in activity upon induction, a level similar to that observed previously with less precise linker scanner mutations. This site had also been shown to be critical for c-Jun mediated NT/N activation, even though c-Jun homodimers do not bind this site in vitro. Therefore, nuclear extracts from PC12 cells were tested for the presence of proteins which could bind this site. Complexes composed of both c-Jun and ATF-2 were found in extracts from both uninduced and induced PC12 cells. ATF-2 could mediate both the recruitment of c-Jun to this site as well as mediate the effect of activators of adenylate cyclase, since ATF-2 has been shown to be a target for protein kinase A in vitro. Expression of ATF-2 in PC12 cells resulted in a modest increase in NT/N promoter activation. The significant levels of endogenous ATF-2 protein in PC12 cells most likely accounts for the relatively small magnitude of this effect. Experiments with the closely related protein, ATF-a2, revealed that it potently antagonizes c-Jun activation while forced expression of ATF-2 did not affect c-Jun activation under the conditions analyzed. Therefore, ATF proteins could be involved in both activation and repression of the NT/N gene. Both c-Jun and ATF-2 have been shown to be activated by c-Jun N-terminal kinase (JNK) in response to environmental stress or cytokine activation. Therefore, the ability of inducers to activate the previously described N-terminal ATF-2 activation domain was investigated using a GAL4-ATF-2 (1-109) chimer construct. This construct was not significantly activated by inducer combinations that result in high level NT/N gene expression, indicating that activation of ATF-2 through this pathway is not involved in NT/N gene activation. Also activation of JNK, a MAPK which activates both c-Jun and ATF-2, only partially substituted for NGF indicating that NGF activates an additional pathway. The data presented here support a model involving synergistic transcriptional activation of the NT/N promoter by c-Jun/c-Fos, ATF-2, ATF-2/c-Jun and the GR. ATF-2 was found to enhance NT/N promoter activation while a splice variant (ATF-2 195) lacking a central portion of ATF-2 that is rich in Ser/Thr residues had no effect suggesting that this region could be important for ATF-2 activation in PC12 cells. The identification of the signaling pathways that mediate the effects of inducer combinations on NT/N gene activation will be an important future goal and should provide insights into the control of neuronal gene expression

Diagnostique sur la Santé des Récifs Coralliens à Nosy Tanikely et la Baie d’Ambanoro

Pendant mon étude, les récifs coralliens à Nosy Tanikely et à la Baie d’Ambanoro étaient examinées avec le but de déterminer la condition de chaque récif et la biomasse des poissons. La durée de cette étude est de trois semaines et j’ai plongé en apnée quatre fois du 10 avril 2009 au 23 avril 2009, pour examiner les trois sites. Il y avait six stations au total, quatre pour examiner le premier site à Nosy Tanikely et deux dans la Baie d’Ambanoro, où sont le deuxième et troisième site. Utilisant les données collectées au long du transect de cent mètres, j’ai calculé l’Indice Condition Récifale et aussi la biomasse des poissons pour déterminer la santé du récif et la richesse des espèces pour chaque site. Les données collectées sur cette étude concernant la condition des récifs coralliens autour de Nosy Be, montrent que les récifs sont en voie de dégradation et sont menaces par les activités anthropiques

RandomClockGamma_50mil

Beast .xml file for Random Clock analysis with 50 million generation

The design of a wearable multi-sensor measurement platform

This thesis provides a complete design of a flexible multi-sensor measurement platform intended for a variety of medical, research, and recreational applications. The design considers practical constraints as a wearable device in a multitude of environments, aiming to satisfy developers', researchers', and users' needs for reliability, power efficiency, ease-of-use, and a functional development environment. This thesis also discusses the evolution through multiple iterations of the device as a response to demand for research and medical applications within the Integrated Microsystems Lab (IML) as well as in collaboration with other groups.The presented platform design delivers several valuable contributions: Firstly, it includes an open-source hardware design for a powerful, compact, multi-sensor measurement platform with a rich user interface. Secondly, to support data logging operations, the design incorporates a novel, extremely lightweight NAND flash file system. Thirdly, a modular, feature-rich, C++-based software framework is built on top of a real-time operating system (RTOS) to provide application developers with the utilities necessary for rapid prototyping. Finally, this framework incorporates an automatic clock- and power-management scheme, allowing for power consumption to be kept at a minimum without burden to the application developer. The platform is capable of measuring inertial parameters such as acceleration and angular movement rate as well as environmental parameters such as magnetic field and barometric pressure. It also contains multiple wired and wireless interfaces to communicate with arbitrary external devices: A sub-GHz wireless interface provides for communicating with continuous glucose monitors (CGMs) as well as any of a growing multitude of Bluetooth-enabled physiological sensors such as heart-rate monitors. Based on a high-performance 168MHz ARM digital signal controller with floating point support, it delivers unprecedented computational throughput for a 3x5cm device drawing as little as 3mW with the RTOS scheduler active.Cette thèse de recherche présente la conception complète d'une plateforme multi-capteur flexible qui est destiné à des applications dans le milieu médical, le milieu de la recherche et à des fins récréatives. Durant la conception, les contraintes associées à des environnements d'utilisations de plusieurs usagers, dont des développeurs, chercheurs et utilisateurs ont étés prises en considération. Les contraintes en termes de fiabilité, d'efficacité énergétique et la facilité d'utilisation ont été prises en compte. Cette thèse discute aussi de l'évolution itérative de la plateforme en réponse aux demandes techniques de la part du « Integrated Microsystems Lab » (IML) et d'autres groupes de recherches pour l'appliquer à des fins médicales et pour la recherche poussée.La plateforme présentée fournie des contributions valables. Premièrement, elle comprend du matériel informatique à source ouvert qui est puissant, compacte, multi-sensoriel, et qui inclut une interface usager riche. De plus, pour supporter l'enregistrement de données, la plateforme comprend un nouveau système de fichiers « flash » qui est extrêmement léger. Troisièmement, elle inclut aussi un environnement de développement modulaire basé sur C++ qui est riche en fonctionnalités et qui est bâtit à partir d'un système d'exploitation en temps-réel. Cet environnement fournira à des développeurs les moyens de prototyper rapidement leur application. Finalement, elle comprend un programme qui gère l'horloge du système ainsi que sa consommation énergétique. Cela permettra de garder la consommation d'énergie au minimum sans encombrer le développeur d'applications.Cette plateforme est capable de mesurer des données d'inertie comme l'accélération et le mouvement angulaire en plus de données environnementales telles que la pression atmosphérique et les champs magnétiques. Elle contient aussi une interface avec/sans-fil permettant la communication à des dispositifs extérieurs arbitraires. Par exemple, une paire d'interfaces sans-fil permet la communication avec des moniteurs de la glycémie en continu ainsi qu'un nombre croissant de capteurs physiologiques Bluetooth tel que les moniteurs cardiaques. La mise en conception du système est faite autour d'un microcontrôleur « ARM » à haute puissance équipé d'un processeur à virgule flottante, ce qui permet à une puissance de calcule sans précédent pour un dispositif d'une taille de 3x5cm qui consomme aussi peu que 3mW même quand le ordonnanceur du système d'exploitation en temps-réel est actif