Self-organized criticality in MHD driven plasma edge turbulence

We analyze long-range time correlations and self-similar characteristics of the electrostatic turbulence at the plasma edge and scrape-off layer in the Tokamak Chauffage Alfven Bresillien (TCABR), with low and high Magnetohydrodynamics (MHD) activity. We find evidence of self-organized criticality (SOC), mainly in the region near the tokamak limiter. Comparative analyses of data before and during the MHD activity reveals that during the high mHD activity the Hurst parameter decreases. Finally, we present a cellular automaton whose parameters are adjusted to simulate the analyzed turbulence SOC change with the MHD activity variation. (C) 2011 Published by Elsevier B.V.

Bifurcation effects on the plasma edge of tokamaks with ergodic limiter.

In the present paper, we solve a twist symplectic map for the action of an ergodic magnetic limiter in a large aspect-ratio tokamak. In this model, we study the bifurcation scenarios that occur in the remnants regular islands that co-exist with chaotic magnetic surfaces. The onset of atypical local bifurcations created by secondary shearless tori are identified through numerical profiles of internal rotation number and we observe that their rupture can reduce the usual magnetic field line escape at the tokamak plasma edge.

Analysis of Electrostatic Turbulence Drive in Texas Helimak.

Plasma turbulence and particle transport in Texas Helimak change with the radial electric field profile modified by an external voltage bias. When the bias is positive, the turbulence shows enhanced level and broadband spectra with extreme events, similar to the turbulence in tokamak scrape-‐off layer. However, negative bias reduces the turbulence level and decreases the spectrum widths. Moreover, for negative biased shots, the particle transport is strongly affected by a wave particle resonant interaction. On the other hand, for positive bias values, the plasma presents a transport barrier in the reversed shear flow region.

A single chain antibody against a viral RNA polymerase (TBSV-BS3-Statice)

Expression of antibodies in plant against essential viral proteins could provide an alternative approach to engineered viral resistance. Engineered single chain Fv antibodies scFV are particularly suitable for expression in plant because of their small size and the lack of assembly requirements. RNA-dependent RNA polymerases (RdRps) function as the catalytic subunit of viral replicases required for the replication of all positive strand RNA viruses. By using Phage technology we selected scFvs from a phage library using purified E.coli expressed TBSV(Tomato bushy stunt virus) replicase as antigen. The scFvs mediated-inhibition of RdRp activity was studied in vitro and in planta. In vitro experiments showed the inhibition of CNV(Cucumber necrosis virus) and TCV(Turnip crinkle virus) RdRp. Transient in planta assays based on agroinfiltration and an infectious clone of TBSV demonstrated the inhibition of the replication of TBSV(Tomato bushy stunt virus). Epitope mapping showed that the selected scFvs target the motif E of RdRp which is involved in template binding.Moreover T1 plants of transgenic lines of N. benthamiana expressing different scFvs either in the cytoplasm or the ER (endoplasmic reticulum) showed a high level of resistance against infection with TBSV and RCNMV(Red clover necrotic mosaic virus) upon inoculation with virus particles. This is the first report that scFvs against a RdRp of a plant viruses can inhibit viral replication in vivo. The resistance is even efficient against viruses belonging to different virus families.

Trasporto di un fascio intenso in un solenoide

Lo scopo di questo lavoro è di studiare il problema del trasporto di una carica attraverso un solenoide. Il campo magnetico ha la caratteristica di essere nullo fuori dal solenoide, costante all’interno, con una transizione più o meno rapida. Quando la transizione è discontinua si può fornire una soluzione analitica associandovi una mappa di trasferimento. Negli altri casi la soluzione si ottiene con una integrazione numerica. Inoltre il solenoide si comporta come una lente cromatica, che può essere usata per selezionare la componente di un fascio con una determinata energia. Nel quadro dei dispositivi che utilizzano solenoidi per focalizzare un fascio di protoni, si descrive il modulo di trasporto a bassa energia denominato LEBT, che precede i dispositivi acceleranti presenti in un linac come quello di ESS. A tal fine si discute brevemente come gli effetti di carica spaziale attenuino il potere focalizzante di un solenoide. Una linea di trasporto LEBT è anche presente nel linac del progetto IFMIF, il cui scopo è analizzare il danneggiamento prodotto dai neutroni sui materiali che verranno impiegati nei reattori ITER e DEMO. In questo abtract non si segue l’ordine di presentazione dei vari argomenti data la diversa rilevanza che questi hanno nella trattazione che segue.

Implementation of the disruption predictor APODIS in JET Real Time Network using the MARTe framework

Disruptions in tokamaks devices are unavoidable, and they can have a significant impact on machine integrity. So it is very important have mechanisms to predict this phenomenon. Disruption prediction is a very complex task, not only because it is a multi-dimensional problem, but also because in order to be effective, it has to detect well in advance the actual disruptive event, in order to be able to use successful mitigation strategies. With these constraints in mind a real-time disruption predictor has been developed to be used in JET tokamak. The predictor has been designed to run in the Multithreaded Application Real-Time executor (MARTe) framework. The predictor ?Advanced Predictor Of DISruptions? (APODIS) is based on Support Vector Machine (SVM).

Contribuciones en sistemas de adquisición de datos inteligentes para entornos de fusión por confinamiento magnético

Los sistemas de adquisición de datos utilizados en los diagnósticos de los dispositivos de fusión termonuclear se enfrentan a importantes retos planteados en los dispositivos de pulso largo. Incluso en los dispositivos de pulso corto, en los que se analizan los datos después de la descarga, existen aún una gran cantidad de datos sin analizar, lo cual supone que queda una gran cantidad de conocimiento por descubrir dentro de las bases de datos existentes. En la última década, la comunidad de fusión ha realizado un gran esfuerzo para mejorar los métodos de análisis off‐line para mejorar este problema, pero no se ha conseguido resolver completamente, debido a que algunos de estos métodos han de resolverse en tiempo real. Este paradigma lleva a establecer que los dispositivos de pulso largo deberán incluir dispositivos de adquisición de datos con capacidades de procesamiento local, capaces de ejecutar avanzados algoritmos de análisis. Los trabajos de investigación realizados en esta tesis tienen como objetivo determinar si es posible incrementar la capacidad local de procesamiento en tiempo real de dichos sistemas mediante el uso de GPUs. Para ello durante el trascurso del periodo de experimentación realizado se han evaluado distintas propuestas a través de casos de uso reales elaborados para algunos de los dispositivos de fusión más representativos como ITER, JET y TCV. Las conclusiones y experiencias obtenidas en dicha fase han permitido proponer un modelo y una metodología de desarrollo para incluir esta tecnología en los sistemas de adquisición para diagnósticos de distinta naturaleza. El modelo define no sólo la arquitectura hardware óptima para realizar dicha integración, sino también la incorporación de este nuevo recurso de procesamiento en los Sistemas de Control de Supervisión y Adquisición de Datos (SCADA) utilizados en la comunidad de fusión (EPICS), proporcionando una solución completa. La propuesta se complementa con la definición de una metodología que resuelve las debilidades detectadas, y permite trazar un camino de integración de la solución en los estándares hardware y software existentes. La evaluación final se ha realizado mediante el desarrollo de un caso de uso representativo de los diagnósticos que necesitan adquisición y procesado de imágenes en el contexto del dispositivo internacional ITER, y ha sido testeada con éxito en sus instalaciones. La solución propuesta en este trabajo ha sido incluida por la ITER IO en su catálogo de soluciones estándar para el desarrollo de sus futuros diagnósticos. Por otra parte, como resultado y fruto de la investigación de esta tesis, cabe destacar el acuerdo llevado a cabo con la empresa National Instruments en términos de transferencia tecnológica, lo que va a permitir la actualización de los sistemas de adquisición utilizados en los dispositivos de fusión. ABSTRACT Data acquisition systems used in the diagnostics of thermonuclear fusion devices face important challenges due to the change in the data acquisition paradigm needed for long pulse operation. Even in shot pulse devices, where data is mainly analyzed after the discharge has finished , there is still a large amount of data that has not been analyzed, therefore producing a lot of buried knowledge that still lies undiscovered in the data bases holding the vast amount of data that has been generated. There has been a strong effort in the fusion community in the last decade to improve the offline analysis methods to overcome this problem, but it has proved to be insufficient unless some of these mechanisms can be run in real time. In long pulse devices this new paradigm, where data acquisition devices include local processing capabilities to be able to run advanced data analysis algorithms, will be a must. The research works done in this thesis aim to determining whether it is possible to increase local capacity for real‐time processing of such systems by using GPUs. For that, during the experimentation period, various proposals have been evaluated through use cases developed for several of the most representative fusion devices, ITER, JET and TCV. Conclusions and experiences obtained have allowed to propose a model, and a development methodology, to include this technology in systems for diagnostics of different nature. The model defines not only the optimal hardware architecture for achieving this integration, but also the incorporation of this new processing resource in one of the Systems of Supervision Control and Data Acquisition (SCADA) systems more relevant at the moment in the fusion community (EPICS), providing a complete solution. The final evaluation has been performed through a use case developed for a generic diagnostic requiring image acquisition and processing for the international ITER device, and has been successfully tested in their premises. The solution proposed in this thesis has been included by the ITER IO in his catalog of standard solutions for the development of their future diagnostics. This has been possible thanks to the technologic transfer agreement signed with xi National Instruments which has permitted us to modify and update one of their core software products targeted for the acquisition systems used in these devices.

Desarrollo de tecnologías de telemanipulación con alto grado de escalado orientadas a la interacción hombre-robot en entornos nucleares

Esta tesis se centra en desarrollo de tecnologías para la interacción hombre-robot en entornos nucleares de fusión. La problemática principal del sector de fusión nuclear radica en las condiciones ambientales tan extremas que hay en el interior del reactor, y la necesidad de que los equipos cumplan requisitos muy restrictivos para poder aguantar esos niveles de radiación, magnetismo, ultravacío, temperatura... Como no es viable la ejecución de tareas directamente por parte de humanos, habrá que utilizar dispositivos de manipulación remota para llevar a cabo los procesos de operación y mantenimiento. En las instalaciones de ITER es obligatorio tener un entorno controlado de extrema seguridad, que necesita de estándares validados. La definición y uso de protocolos es indispensable para regir su buen funcionamiento. Si nos centramos en la telemanipulación con algo grado de escalado, surge la necesidad de definir protocolos para sistemas abiertos que permitan la interacción entre equipos y dispositivos de diversa índole. En este contexto se plantea la definición del Protocolo de Teleoperación que permita la interconexión entre dispositivos maestros y esclavos de distinta tipología, pudiéndose comunicar bilateralmente entre sí y utilizar distintos algoritmos de control según la tarea a desempeñar. Este protocolo y su interconectividad se han puesto a prueba en la Plataforma Abierta de Teleoperación (P.A.T.) que se ha desarrollado e integrado en la ETSII UPM como una herramienta que permita probar, validar y realizar experimentos de telerrobótica. Actualmente, este Protocolo de Teleoperación se ha propuesto a través de AENOR al grupo ISO de Telerobotics como una solución válida al problema existente y se encuentra bajo revisión. Con el diseño de dicho protocolo se ha conseguido enlazar maestro y esclavo, sin embargo con los niveles de radiación tan altos que hay en ITER la electrónica del controlador no puede entrar dentro del tokamak. Por ello se propone que a través de una mínima electrónica convenientemente protegida se puedan multiplexar las señales de control que van a través del cableado umbilical desde el controlador hasta la base del robot. En este ejercicio teórico se demuestra la utilidad y viabilidad de utilizar este tipo de solución para reducir el volumen y peso del cableado umbilical en cifras aproximadas de un 90%, para ello hay que desarrollar una electrónica específica y con certificación RadHard para soportar los enormes niveles de radiación de ITER. Para este manipulador de tipo genérico y con ayuda de la Plataforma Abierta de Teleoperación, se ha desarrollado un algoritmo que mediante un sensor de fuerza/par y una IMU colocados en la muñeca del robot, y convenientemente protegidos ante la radiación, permiten calcular las fuerzas e inercias que produce la carga, esto es necesario para poder transmitirle al operador unas fuerzas escaladas, y que pueda sentir la carga que manipula, y no otras fuerzas que puedan influir en el esclavo remoto, como ocurre con otras técnicas de estimación de fuerzas. Como el blindaje de los sensores no debe ser grande ni pesado, habrá que destinar este tipo de tecnología a las tareas de mantenimiento de las paradas programadas de ITER, que es cuando los niveles de radiación están en sus valores mínimos. Por otro lado para que el operador sienta lo más fielmente posible la fuerza de carga se ha desarrollado una electrónica que mediante el control en corriente de los motores permita realizar un control en fuerza a partir de la caracterización de los motores del maestro. Además para aumentar la percepción del operador se han realizado unos experimentos que demuestran que al aplicar estímulos multimodales (visuales, auditivos y hápticos) aumenta su inmersión y el rendimiento en la consecución de la tarea puesto que influyen directamente en su capacidad de respuesta. Finalmente, y en referencia a la realimentación visual del operador, en ITER se trabaja con cámaras situadas en localizaciones estratégicas, si bien el humano cuando manipula objetos hace uso de su visión binocular cambiando constantemente el punto de vista adecuándose a las necesidades visuales de cada momento durante el desarrollo de la tarea. Por ello, se ha realizado una reconstrucción tridimensional del espacio de la tarea a partir de una cámara-sensor RGB-D, lo cual nos permite obtener un punto de vista binocular virtual móvil a partir de una cámara situada en un punto fijo que se puede proyectar en un dispositivo de visualización 3D para que el operador pueda variar el punto de vista estereoscópico según sus preferencias. La correcta integración de estas tecnologías para la interacción hombre-robot en la P.A.T. ha permitido validar mediante pruebas y experimentos para verificar su utilidad en la aplicación práctica de la telemanipulación con alto grado de escalado en entornos nucleares de fusión. Abstract This thesis focuses on developing technologies for human-robot interaction in nuclear fusion environments. The main problem of nuclear fusion sector resides in such extreme environmental conditions existing in the hot-cell, leading to very restrictive requirements for equipment in order to deal with these high levels of radiation, magnetism, ultravacuum, temperature... Since it is not feasible to carry out tasks directly by humans, we must use remote handling devices for accomplishing operation and maintenance processes. In ITER facilities it is mandatory to have a controlled environment of extreme safety and security with validated standards. The definition and use of protocols is essential to govern its operation. Focusing on Remote Handling with some degree of escalation, protocols must be defined for open systems to allow interaction among different kind of equipment and several multifunctional devices. In this context, a Teleoperation Protocol definition enables interconnection between master and slave devices from different typologies, being able to communicate bilaterally one each other and using different control algorithms depending on the task to perform. This protocol and its interconnectivity have been tested in the Teleoperation Open Platform (T.O.P.) that has been developed and integrated in the ETSII UPM as a tool to test, validate and conduct experiments in Telerobotics. Currently, this protocol has been proposed for Teleoperation through AENOR to the ISO Telerobotics group as a valid solution to the existing problem, and it is under review. Master and slave connection has been achieved with this protocol design, however with such high radiation levels in ITER, the controller electronics cannot enter inside the tokamak. Therefore it is proposed a multiplexed electronic board, that through suitable and RadHard protection processes, to transmit control signals through an umbilical cable from the controller to the robot base. In this theoretical exercise the utility and feasibility of using this type of solution reduce the volume and weight of the umbilical wiring approximate 90% less, although it is necessary to develop specific electronic hardware and validate in RadHard qualifications in order to handle huge levels of ITER radiation. Using generic manipulators does not allow to implement regular sensors for force feedback in ITER conditions. In this line of research, an algorithm to calculate the forces and inertia produced by the load has been developed using a force/torque sensor and IMU, both conveniently protected against radiation and placed on the robot wrist. Scaled forces should be transmitted to the operator, feeling load forces but not other undesirable forces in slave system as those resulting from other force estimation techniques. Since shielding of the sensors should not be large and heavy, it will be necessary to allocate this type of technology for programmed maintenance periods of ITER, when radiation levels are at their lowest levels. Moreover, the operator perception needs to feel load forces as accurate as possible, so some current control electronics were developed to perform a force control of master joint motors going through a correct motor characterization. In addition to increase the perception of the operator, some experiments were conducted to demonstrate applying multimodal stimuli (visual, auditory and haptic) increases immersion and performance in achieving the task since it is directly correlated with response time. Finally, referring to the visual feedback to the operator in ITER, it is usual to work with 2D cameras in strategic locations, while humans use binocular vision in direct object manipulation, constantly changing the point of view adapting it to the visual needs for performing manipulation during task procedures. In this line a three-dimensional reconstruction of non-structured scenarios has been developed using RGB-D sensor instead of cameras in the remote environment. Thus a mobile virtual binocular point of view could be generated from a camera at a fixed point, projecting stereoscopic images in 3D display device according to operator preferences. The successful integration of these technologies for human-robot interaction in the T.O.P., and validating them through tests and experiments, verify its usefulness in practical application of high scaling remote handling at nuclear fusion environments.

T cell vaccination induces T cell receptor Vβ-specific Qa-1-restricted regulatory CD8+ T cells

Vaccination of mice with activated autoantigen-reactive CD4+ T cells (T cell vaccination, TCV) has been shown to induce protection from the subsequent induction of a variety of experimental autoimmune diseases, including experimental allergic encephalomyelitis (EAE). Although the mechanisms involved in TCV-mediated protection are not completely known, there is some evidence that TCV induces CD8+ regulatory T cells that are specific for pathogenic CD4+ T cells. Previously, we demonstrated that, after superantigen administration in vivo, CD8+ T cells emerge that preferentially lyse and regulate activated autologous CD4+ T cells in a T cell receptor (TCR) Vβ-specific manner. This TCR Vβ-specific regulation is not observed in β2-microglobulin-deficient mice and is inhibited, in vitro, by antibody to Qa-1. We now show that similar Vβ8-specific Qa-1-restricted CD8+ T cells are also induced by TCV with activated CD4+ Vβ8+ T cells. These CD8+ T cells specifically lyse murine or human transfectants coexpressing Qa-1 and murine TCR Vβ8. Further, CD8+ T cell hybridoma clones generated from B10.PL mice vaccinated with a myelin basic protein-specific CD4+Vβ8+ T cell clone specifically recognize other CD4+ T cells and T cell tumors that express Vβ8 and the syngeneic Qa-1a but not the allogeneic Qa-1b molecule. Thus, Vβ-specific Qa-1-restricted CD8+ T cells are induced by activated CD4+ T cells. We suggest that these CD8+ T cells may function to specifically regulate activated CD4+ T cells during immune responses.

Compact stellarators with modular coils

Compact stellarator designs with modular coils and only two or three field periods are now available; these designs have both good stability and quasiaxial symmetry providing adequate transport for a magnetic fusion reactor. If the bootstrap current assumes theoretically predicted values a three field period configuration is optimal, but if that net current turns out to be lower, a device with two periods and just 12 modular coils might be better. There are also attractive designs with quasihelical symmetry and four or five periods whose properties depend less on the bootstrap current. Good performance requires that there be a satisfactory magnetic well in the vacuum field, which is a property lacking in a stellarator-tokamak hybrid that has been proposed for a proof of principle experiment. In this paper, we present an analysis of stability for these configurations that is based on a mountain pass theorem asserting that, if two solutions of the problem of magnetohydrodynamic equilibrium can be found, then there has to be an unstable solution. We compare results of our theory of equilibrium, stability, and transport with recently announced measurements from the large LHD experiment in Japan.

Análise nutricional de dietas publicadas em revistas não científicas destinadas ao público feminino

A procura do corpo ideal está fortemente ligada à perda de peso, sendo insistentemente abordada na comunicação social, a imagem corporal, têm conotações mais relacionadas com a moda do que com verdadeiros riscos para a saúde das pessoas. A sociedade atual cultiva a boa aparência física, "o conhecido estar em forma", associada a um ideal estético de magreza e, ao mesmo tempo, apela ao consumo de alimentos de elevada densidade calórica. Na busca do corpo ideal, as dietas de emagrecimento publicadas nas revistas poderão ser uma ajuda na concretização deste objetivo. É fácil encontrar em qualquer quiosque, papelaria ou supermercado estrategicamente colocadas, inúmeras revistas que atribuem à imagem corporal honras de primeira página. Na verdade, estas revistas não científicas divulgam dietas para todos os gostos e situações: dietas específicas para emagrecimento localizado, dietas de preparação para a praia ou para corrigir excessos cometidos em épocas festivas. Embora sabendo-se que estas “auto –dietas” constituem um dos métodos mais utilizados para a perda de peso corporal, não se sabe o número de seguidores que elas têm atualmente. Neste contexto, uma vez que a maior delas não contêm informação nutricional, é importante estar alerta para alguns problemas que podem resultar da ingestão recorrente e sem supervisão deste tipo de dietas. Neste âmbito e dada a pertinência do tema, constituiu objetivo principal do presente trabalho, a análise nutricional de dietas publicadas em revistas não científicas, destinadas ao público feminino em termos de macronutrientes e micronutrientes, sendo também considerado o número de refeições/dia e a variedade de alimentos recomendados. Assim, foram analisadas 15 dietas (497 refeições) publicadas em revistas destinadas ao público feminino, adquiridas entre o ano de 2009 e 2011. A conversão de alimentos em nutrientes foi feita através dos programas informáticos MedPoint e FatSecret. As dietas apresentaram valores energéticos totais (V.E.T.) médios diários, compreendidos entre 378,0 ± 53,8 Kcal e 2335,0 ± 135,0 Kcal. A avaliação dos macronutrientes revelou um teor proteico entre os 32,0 ± 3,6 % e os 12,0 ± 0,1% do total energético Os hidratos de carbono oscilaram entre 63,0 ± 0,1% e 43,0 ± 3,6%. Já a dieta mais rica em lípidos totais apresentava um valor médio de 32,0 ± 9,3% contra os 14,0 ± 0,1% do valor mais baixo encontrado. Nenhuma das dietas assegurava o valor recomendado de ingestão de fibra quando comparada com a dose diária recomendável (DDR). Relativamente à análise dos micronutrientes (vitamina D, vitamina E; vitamina C; vitamina B2, Ácido fólico, cálcio, fósforo, ferro, zinco), somente um tipo de dieta apresentou valores médios diários concordantes com as recomendações preconizadas. Considerando que as dietas analisadas tinham como objetivo a perda rápida de peso, estas revelaram-se maioritariamente hipocalóricas apresentando desequilíbrios e carências de determinados macronutrientes e micronutrientes que poderão, quando mantidas num período de tempo alargado ter consequências graves no desenvolvimento de carência ou outras patologias.

DESEMPENHO HIDRÁULICO DE EXUTORES SUBMARINOS

Nos centros urbanos próximos das orlas marítimas, tem-se optado pela descarga de águas residuais para o mar, aproveitando-se da elevada capacidade de depuração do oceano. Neste trabalho coloca-se o seguinte desafio: será possível um programa usado para a modelação de rede de distribuição de água ser capaz de modelar um exutor submarino? Para responder a este desafio, recorreu-se a um conjunto de artifícios, tendo por base conhecimentos da hidráulica. Foi construído um modelo unidimensional usando o EPANET cujas fronteiras são: a montante, a Câmara de Carga, a jusante os difusores. Recorreu-se aos componentes do EPANET, tais como: válvulas TCV (Throttle Control Valve) e reservatórios de nível fixo para simular a descarga e o nível de maré respetivamente. A modelação hidráulica de um exutor submarino tem implicações no impacto da descarga pelo que torna-se necessário o estudo da diluição inicial conseguida numa descarga. No presente trabalho desenvolveu-se um programa EPANET / MatLab com o objetivo de facilitar a aplicação desses artifícios e de estimar a diluição inicial. Aplicou-se o programa desenvolvido num caso de estudo e utilizou-se a versão beta do CORHYD, usado em obras de engenharia com alguma importância, para validar os resultados obtido através do programa EPANET /MatLab.

STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3´ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES

Turnip crinkle virus (TCV) and Pea enation mosaic virus (PEMV) are two positive (+)-strand RNA viruses that are used to investigate the regulation of translation and replication due to their small size and simple genomes. Both viruses contain cap-independent translation elements (CITEs) within their 3´ untranslated regions (UTRs) that fold into tRNA-shaped structures (TSS) according to nuclear magnetic resonance and small angle x-ray scattering analysis (TCV) and computational prediction (PEMV). Specifically, the TCV TSS can directly associate with ribosomes and participates in RNA-dependent RNA polymerase (RdRp) binding. The PEMV kissing-loop TSS (kl-TSS) can simultaneously bind to ribosomes and associate with the 5´ UTR of the viral genome. Mutational analysis and chemical structure probing methods provide great insight into the function and secondary structure of the two 3´ CITEs. However, lack of 3-D structural information has limited our understanding of their functional dynamics. Here, I report the folding dynamics for the TCV TSS using optical tweezers (OT), a single molecule technique. My study of the unfolding/folding pathways for the TCV TSS has provided an unexpected unfolding pathway, confirmed the presence of Ψ3 and hairpin elements, and suggested an interconnection between the hairpins and pseudoknots. In addition, this study has demonstrated the importance of the adjacent upstream adenylate-rich sequence for the formation of H4a/Ψ3 along with the contribution of magnesium to the stability of the TCV TSS. In my second project, I report on the structural analysis of the PEMV kl-TSS using NMR and SAXS. This study has re-confirmed the base-pair pattern for the PEMV kl-TSS and the proposed interaction of the PEMV kl-TSS with its interacting partner, hairpin 5H2. The molecular envelope of the kl-TSS built from SAXS analysis suggests the kl-TSS has two functional conformations, one of which has a different shape from the previously predicted tRNA-shaped form. Along with applying biophysical methods to study the structural folding dynamics of RNAs, I have also developed a technique that improves the production of large quantities of recombinant RNAs in vivo for NMR study. In this project, I report using the wild-type and mutant E.coli strains to produce cost-effective, site-specific labeled, recombinant RNAs. This technique was validated with four representative RNAs of different sizes and complexity to produce milligram amounts of RNAs. The benefit of using site-specific labeled RNAs made from E.coli was demonstrated with several NMR techniques.

Alternate Conformations Regulate Ribosomal Recoding in a Positive-sense RNA Virus

Positive-sense RNA viruses are important animal, plant, insect and bacteria pathogens and constitute the largest group of RNA viruses. Due to the relatively small size of their genomes, these viruses have evolved a variety of non-canonical translation mechanisms to optimize coding capacity expanding their proteome diversity. One such strategy is codon redefinition or recoding. First described in viruses, recoding is a programmed translation event in which codon alterations are context dependent. Recoding takes place in a subset of messenger RNA (mRNAs) with some products reflecting new, and some reflecting standard, meanings. The ratio between the two is both critical and highly regulated. While a variety of recoding mechanisms have been documented, (ribosome shunting, stop-carry on, termination-reinitiation, and translational bypassing), the two most extensively employed by RNA viruses are Programmed Ribosomal Frameshifting (PRF) and Programmed Ribosomal Readthrough (PRT). While both PRT and PRF subvert normal decoding for expression of C-terminal extension products, the former involves an alteration of reading frame, and the latter requires decoding of a non-sense codon. Both processes occur at a low but defined frequency, and both require Recoding Stimulatory Elements (RSE) for regulation and optimum functionality. These stimulatory signals can be embedded in the RNA in the form of sequence or secondary structure, or trans-acting factors outside the mRNA such as proteins or micro RNAs (miRNA). Despite 40+ years of study, the precise mechanisms by which viral RSE mediate ribosome recoding for the synthesis of their proteins, or how the ratio of these products is maintained, is poorly defined. This study reveals that in addition to a long distance RNA:RNA interaction, three alternate conformations and a phylogenetically conserved pseudoknot regulate PRT in the carmovirus Turnip crinkle virus (TCV).

Jornalismo no periodo eleitoral: legislativas 2016

O presente trabalho de conclusão do curso de licenciatura em Ciência Política e Relações Internacionais visa entender a relevância do jornalismo em tempo de eleições. Durante as campanhas eleitorais, os meios de comunicação social, além de assumirem um papel de suma importância, apresentam como uma das suas finalidades aproximar a sociedade e os candidatos a cargos políticos, de modo a terem maior e melhor percepção dos mesmos. Com base num estudo de caso direcionado à cobertura das eleições legislativas de 2016, pretende-se analisar a forma como os órgãos de comunicação social cabo-verdianos, em especial a imprensa, trabalharam o tema. O presente trabalho visa estudar os suportes mediáticos (jornais impressos, RCV e TCV) utilizados ao longo das campanhas eleitorais para as legislativas de 2016, no primeiro momento iremos estudar estes suportes e de uma forma mais detalhada e num segundo momento iremos fazer uma análise das entrevistas feitas aos políticos e aos jornalistas. Os meios da comunicação social em particular os jornais impressos de uma forma geral não dão a mesmas atenção a todas as candidaturas ao longo da campanha eleitoral, ou seja dao mais visbilidade aos partidos com mais possibilidade de ganhar as eleições.