No description available.

Thesis (M.S.); Submitted to the Univ. of South Carolina, Columbia, SC (US); 1 Apr 2003. / Published through the Information Bridge: DOE Scientific and Technical Information. "JLAB-PHY-03-37" "DOE/ER/40150-2740" Clarisse Tur. 04/01/2003. Report is also available in paper and microfiche from NTIS.

No description available.

Alix (ALG-2 Interacting Protein X) est une protéine cytoplasmique impliquée dans divers processus cellulaires allant de l'apoptose à la cytocinèse en passant par le bourgeonnement des virus, la réparation membranaire et la régulation de la voie endosomale. Toutes ces fonctions sont étroitement associées à l'interaction d'Alix avec ses partenaires impliqués dans la déformation des membranes telles que les endophilines A, Tsg-101 et CHMP4B du complexe ESCRT (Endosomal Sorting Complex Required for Transport). Le but de ce projet est de caractériser le phénotype de la souris Alix ko récemment développée au laboratoire, dans l'espoir de mieux comprendre le rôle physiologique d'Alix. Ces souris, viables et fertiles, sont caractérisées par une microcéphalie apparaissant au cours de l'embryogenèse. Ce phénotype est accompagné d'une apoptose massive touchant les progéniteurs neuronaux durant la neurogenèse et d'une altération du développement de l'arborisation dendritique après la naissance. Les souris adultes présentent également des défauts de plasticité synaptique accompagnés d'une altération du recyclage des vésicules synaptiques. L'ensemble de ces processus repose sur la capacité d'Alix à contrôler le remodelage de la membrane plasmique. Au niveau moléculaire, nos travaux sur les neurones en cultures et sur les fibroblastes montrent une régulation de l'endocytose indépendante de la clathrine (CIE) par Alix et les endophilines A qui pourrait être à l'origine du phénotype neuronal de la souris. Cependant, l'association d'Alix avec CHMP4B du complexe ESCRT pourrait également être nécessaire au développement du système nerveux puisque l'interaction Alix-CHMP4B est nécessaire pour le contrôle de la CIE et de la mort neuronale.L'ensemble de ces résultats mets en évidence qu'à travers des mécanismes et des partenaires bien caractérisés, Alix est requise pour de nouvelles fonctions nécessaires au développement et au fonctionnement du système nerveux. / Alix (ALG-2 Interacting Protein X) is a cytoplasmic protein implicated in multiple processes including apoptosis, endosome function, membrane repair, viral budding and cytokinesis. Most of these involve modifications of plasma or endosomal membrane organization. Consistent with this, Alix is known to interact with diverse proteins modulating membrane deformation, such as endophilins or Tsg-101 and CHMP4B of the Endosomal Sorting Complex Required for Transport (ESCRT). By studying the phenotype of Alix ko mice that we recently developed, we aim to better understand the precise role of Alix in vivo. These mice are viable and fertile but develop microcephaly even at embryonic stages. This microcephaly is associated with an increase of apoptosis in neural progenitor cells in embryos and a defect in neurite outgrowth at post-natal stages. Later on, these mice also develop defects in synaptic plasticity related to an alteration of synaptic vesicle recycling. All of these processes are tightly dependent on membrane shaping and remodelling. These features of the phenotype can be related to a new function of Alix with endophilin A in the control of clathrin-independent endocytosis (CIE), as described in Alix ko fibroblasts and cultured neurons. However, these defects might also be related to the well-known Alix partner CHMP4B, since we now know that this interaction is needed for controlling CIE and neuronal cell death.All together, these results shed light on novel functions of Alix in the developing and adult central nervous system, all relying on well-known molecular mechanisms and partners.

Les modèles de mutations décrivent le processus d’apparitions rares et aléatoires de mutations au cours de lacroissance d’une population de cellules. Les échantillons obtenus sont constitués de nombres finaux de cellules mutantes,qui peuvent être couplés avec des nombres totaux de cellules ou un nombre moyen de cellules en fin d’expérience.La loi du nombre final de mutantes est une loi à queue lourde : de grands décomptes, appelés “jackpots”,apparaissent fréquemment dans les données.Une construction générale des modèles se décompose en troisniveaux. Le premier niveau est l’apparition de mutations aléatoires au cours d’un processus de croissance de population.En pratique, les divisions cellulaires sont très nombreuses, et la probabilité qu’une de ces divisions conduise à une mutation est faible,ce qui justifie une approximation poissonnienne pour le nombre de mutations survenant pendant un temps d’observation donné.Le second niveau est celui des durées de développement des clones issus de cellules mutantes. Du fait de la croissance exponentielle,la majeure partie des mutations ont lieu à la fin du processus, et les durées de développement sont alors indépendanteset exponentiellement distribuées. Le troisième niveau concerne le nombre decellules qu’un clone issu d’une cellule mutante atteint pendant une durée de développement donnée.La loi de ce nombre dépend principalement de la loi des instants de division des mutantes.Le modèle classique, dit de Luria-Delbrück, suppose que les développements cellulaires des cellules normales aussi bien que mutantess’effectue selon un processus de Yule. On peut dans ce cas calculer expliciter la loi du nombre final de mutantes.Elle dépend de deux paramètres, qui sont le nombre moyen de mutations et le paramètre de fitness (ratio des taux de croissance des deux types de cellules).Le problème statistique consiste à estimer ces deux paramètres au vu d’un échantillon denombres finaux de mutantes. Il peut être résolu par maximisation de la vraisemblance,ou bien par une méthode basée sur la fonction génératrice. Diviser l'estimation du nombre moyen de mutations par le nombre total de cellulespermet alors d'estimer la probabilité d’apparition d’une mutation au cours d’une division cellulaire.L’estimation de cette probabilité est d’une importancecruciale dans plusieurs domaines de la médecine et debiologie: rechute de cancer, résistance aux antibiotiques de Mycobacterium Tuberculosis, etc.La difficulté provient de ce que les hypothèses de modélisation sous lesquelles la distribution du nombre final de mutants est explicitesont irréalistes.Or estimer les paramètres d’un modèle quand la réalité en suit un autre conduit nécessairement à un biais d’estimation.Il est donc nécessaire de disposer de méthodes d’estimation robustes pour lesquelles le biais, en particulier sur la probabilité de mutation,reste le moins sensible possible aux hypothèses de modélisation.Cette thèse contient une étude probabiliste et statistique de modèles de mutations prenant en compte les sources de biais suivantes : durées de vie non exponentielles, morts cellulaires,variabilité du nombre final de cellules, durées de vie non-exponentielles et non-identiquement distribuées, dilution de la population initiale.Des études par simulation des méthodes considérées sont effectuées afin de proposer, selon les caractéristiques du modèle,l’estimation la plus fiable possible. Ces méthodes ont également été appliquées à desjeux de données réelles, afin de comparer les résultats avec les estimations obtenues avec les modèles classiques.Un package R a été implémenté en collaboration avec Rémy Drouilhet et Stéphane Despréaux et est disponible sur le CRAN.Ce package est constitué des différents résultats obtenus au cours de ce travail. Il contient des fonctions dédiées aux modèles de mutations,ainsi qu'à l'estimation des paramètres. Les applications ont été développées pour le Labex TOUCAN (Toulouse Cancer). / Mutation models are probabilistic descriptions of the growth of a population of cells, where mutationsoccur randomly during the process. Data are samples of integers, interpreted as final numbers ofmutant cells. These numbers may be coupled with final numbers of cells (mutant and non mutant) or a mean final number of cells.The frequent appearance in the data of very large mutant counts, usually called “jackpots”, evidencesheavy-tailed probability distributions.Any mutation model can be interpreted as the result of three ingredients. The first ingredient is about the number of mutations occuring with small probabilityamong a large number of cell divisions. Due to the law of small numbers, the number of mutations approximately follows aPoisson distribution. The second ingredient models the developing duration of the clone stemming from each mutation. Due to exponentialgrowth, most mutations occur close to the end of the experiment. Thus the developing time of arandom clone has exponential distribution. The last ingredients represents the number of mutant cells that any clone developing for a given time will produce. Thedistribution of this number depends mainly on the distribution of division times of mutants.One of the most used mutation model is the Luria-Delbrück model.In these model, division times of mutant cells were supposed to be exponentially distributed.Thus a clone develops according to a Yule process and its size at any given time follows a geometric distribution.This approach leads to a family of probability distributions which depend on the expected number of mutations and the relative fitness, which is the ratio between the growth rate of normal cells to that of mutants.The statistic purpose of these models is the estimation of these parameters. The probability for amutant cell to appear upon any given cell division is estimated dividing the mean number of mutations by the mean final number of cells.Given samples of final mutant counts, it is possible to build estimators maximizing the likelihood, or usingprobability generating function.Computing robust estimates is of crucial importance in medical applications, like cancer tumor relapse or multidrug resistance of Mycobacterium Tuberculosis for instance.The problem with classical mutation models, is that they are based on quite unrealistic assumptions: constant final number of cells,no cell deaths, exponential distribution of lifetimes, or time homogeneity. Using a model for estimation, when thedata have been generated by another one, necessarily induces a bias on estimates.Several sources of bias has been partially dealed until now: non-exponential lifetimes, cell deaths, fluctuations of the final count of cells,dependence of the lifetimes, plating efficiency. The time homogeneity remains untreated.This thesis contains probabilistic and statistic study of mutation models taking into account the following bias sources:non-exponential and non-identical lifetimes, cell deaths, fluctuations of the final count of cells, plating efficiency.Simulation studies has been performed in order to propose robust estimation methods, whatever the modeling assumptions.The methods have also been applied to real data sets, to compare the results with the estimates obtained under classical models.An R package based on the different results obtained in this work has been implemented (joint work with Rémy Drouilhetand Stéphane Despréaux) and is available on the CRAN. It includes functions dedicated to the mutation models and parameter estimation.The applications have been developed for the Labex TOUCAN (Toulouse Cancer).

Made available in DSpace on 2014-10-09T12:41:56Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:04:33Z (GMT). No. of bitstreams: 0 / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Submitted by Riscelly Santana Magalhães (riscellysm@yahoo.com.br) on 2018-04-17T14:08:44Z No. of bitstreams: 1 RISCELLY S MAGALHAES DISSERTAÇAO FINAL.pdf: 932501 bytes, checksum: c2d917ba32666cdb1776d82a3adf6c77 (MD5) / Approved for entry into archive by Maria Lucia Martins Frederico null (mlucia@fca.unesp.br) on 2018-04-17T15:32:45Z (GMT) No. of bitstreams: 1 magalhaes_rs_me_botfca.pdf: 878435 bytes, checksum: d236e45a87a39b3f6a57ac5f8dbbefb5 (MD5) / Made available in DSpace on 2018-04-17T15:32:45Z (GMT). No. of bitstreams: 1 magalhaes_rs_me_botfca.pdf: 878435 bytes, checksum: d236e45a87a39b3f6a57ac5f8dbbefb5 (MD5) Previous issue date: 2018-03-06 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / As brássicas são hortaliças de importante valor econômico, bem como boa fonte de minerais, vitaminas e de substâncias com propriedades anticarcinogênicas. O romanesco é uma hortaliça herbácea, com anatomia muito parecida à de brócolis e couve-flor, sendo mais tenra que a couve-flor. Foram realizados dois experimentos. No primeiro, objetivou-se avaliar a efetividade do uso de atmosfera modificada passiva na manutenção da qualidade pós-colheita do romanesco através das avaliações físico-químicas dos mesmos, mantidos sob refrigeração. No segundo, faz-se uma comparação entre as brássicas: romanesco, couve-de-folha, couve-flor, brócolis ramoso e brócolis de inflorescência única. No primeiro experimento foram realizados os seguintes tratamentos: T1: armazenamento em bandeja de poliestireno expandido sem filme; T2: armazenamento em bandeja de poliestireno expandido recoberta com filme de policloreto de vinila (PVC); T3: armazenamento em filme plástico de polietileno de baixa densidade (PEBD) de 0,6µ; T4: armazenamento em filme plástico de polietileno de baixa densidade (PEBD) de 0,8µ. Após a realização dos tratamentos os romanescos foram armazenados em câmara fria a temperatura de 5 ± 1 °C e UR entre 80 ± 5 % durante 16 dias, sendo avaliados de quatro em quatro dias. Utilizaram-se seis repetições por tratamento. Neste experimento foram realizadas as seguintes avaliações físico-químicas: teores de macronutrientes das folhas e inflorescências, perda de massa, sólidos solúveis, potencial hidrogeniônico (pH), acidez titulável, ácido ascórbico, açúcares redutores, clorofila a e b, antocianina e carotenoides. No segundo experimento foram avaliadas as características físico-químicas: número de folhas por planta; massa da matéria fresca das folhas; massa da matéria fresca da inflorescência; diâmetro transversal da inflorescência, circunferência da inflorescência, massa do ramo sem caule, sólidos solúveis, potencial hidrogeniônico (pH), acidez titulável, ácido ascórbico (exceto couve-de-folha), clorofila a e b, antocianina, carotenoides, açúcares redutores, proteína bruta, cinza, umidade, lipídeos e fibra bruta. Foi realizada análise de variância, teste de Tukey considerando-se um nível de significância p˂0,05, média e desvio padrão. Observou-se que para as características sólidos solúveis, pH, acidez titulável e ácido ascórbico, a utilização de filmes plásticos foi importante para a conservação e manutenção das características do romanesco, a partir do 12° dia de armazenamento, enquanto que para açúcares redutores, clorofila a e b, antocianina e carotenoides, foi importante em todos os tratamentos e dias de armazenamento. Para a perda de massa, a utilização de filmes plásticos foi essencial para a conservação do romanesco, possibilitando a viabilidade comercial do produto final. Para o número de folhas por planta; massa da matéria fresca das folhas; massa da matéria fresca da inflorescência; diâmetro transversal da inflorescência, circunferência da inflorescência e massa do ramo sem caule, as médias variaram, com exceção do número de folhas por planta e massa da matéria fresca das folhas do romanesco, quando comparado as demais brássicas. Para sólidos solúveis, pH, acidez titulável, pigmentos, açúcares redutores, proteína bruta, cinza, umidade, lipídeos e fibra bruta, foram observadas diferenças significativas entre as brássicas avaliadas. / The brassicas are vegetables of important economic value, as well as good source of minerals, vitamins and substances with anticarcinogenic properties. The romanesco is an herbaceous vegetable, with anatomy very similar to that of broccoli and cauliflower, being tenderer than cauliflower. Two experiments were carried out. In the first one, the objective was to evaluate the effectiveness of the use of passive modified atmosphere in the maintenance of post-harvest quality of the romanesco through the physical-chemical evaluations of the same, kept under refrigeration. In the second, a comparison is made between the brassicas: romanesco, cabbage leaf, cauliflower, branchy broccoli, and single inflorescence broccoli. In the first experiment the following treatments were performed: T1: tray storage of expanded polystyrene without film; T2: tray storage of expanded polystyrene coated with polyvinyl chloride (PVC) film; T3: storage of low density polyethylene (LDPE) film of 0.6μ; T4: low density polyethylene plastic film (LDPE) of 0.8μ. After the treatments, the romanescos were stored in a cold room at 5 ± 1 ° C and RH at 80 ± 5% for 16 days and evaluated every four days. Six replicates were used per treatment. In this experiment the following physical and chemical evaluations were performed: macronutrient contents of leaves and inflorescences, loss of mass, soluble solids, hydrogenation potential (pH), titratable acidity, ascorbic acid, reducing sugars, chlorophyll a and b, anthocyanin and carotenoids. In the second experiment the physical-chemical characteristics were evaluated: number of leaves per plant; mass of fresh leaf matter; mass of fresh inflorescence matter; (pH), titratable acidity, ascorbic acid (except leaf kale), chlorophyll a and b, anthocyanin, carotenoids, reducing sugars, crude protein , ash, moisture, lipids and crude fiber. A variance analysis was performed, Tukey's test considering a level of significance p˂0.05, mean and standard deviation. It was observed that for the soluble solid characteristics, pH, titratable acidity and ascorbic acid, the use of plastic films was important for the preservation and maintenance of the characteristics of the romanesco, from the 12 day of storage, whereas for reducing sugars, chlorophyll a and b, anthocyanin and carotenoids, was important in all treatments and storage days. For the loss of mass, the use of plastic films was essential for the preservation of the romanesco, allowing the commercial viability of the final product. For the number of leaves per plant; mass of fresh leaf matter; mass of fresh inflorescence matter; the transverse diameter of the inflorescence, the circumference of the inflorescence and the mass of the stem less branch, the averages varied, except for the number of leaves per plant and fresh matter mass of the leaves of the romanesco, when compared to the other brassicas. For soluble solids, pH, titratable acidity, pigments, reducing sugars, crude protein, ash, moisture, lipids and crude fiber, significant differences were observed among the evaluated brassicas.

Les ARNnc sont impliqués dans la régulation de l’expression des gènes via divers mécanismes. Ils adoptent des structures 3D composées à 70% de pb WC formant des hélices de types A liées entre elles par des jonctions modulaires ayant des caractéristiques géométriques spécifiques. Nous avons identifié un nouveau motif 3D d’ARN apparenté au kturn, le pk-turn. Le pk-turn, situé dans la RNase P bactérienne permet, comme le k-turn, la formation d’un angle de 60° entre les hélices P16 & P17 avec cependant des exigences de séquences et de structure différentes. Le 2nd ribozyme qui a focalisé mon attention est le LCrz observé dans l’intron siamois (GIR2/LCrz) identifié dans le pré-ARNr 18S de la petite sous unité du ribosome eucaryote du myxomycète D. iridis. LCrz catalyse une réaction de branchement, équivalente à la première étape de l’épissage par les introns de groupe II, dans un contexte structural proche des introns du groupe I. Nous avons résolu la structure cristallographique du LCrz à une résolution de 2.5Å révélant un repliement inattendu. Cette structure a été confirmée par des expériences de SAXS. Ce travail nous permet de souligner la relation entre structure et fonction dans l'évolution des ribozymes. / NcRNA represent most of primary transcripts RNA in higher eukaryotes and tune gene expression via diverse mechanisms. They adopt 3D structures composed at 70% by WC bp forming A-form helices linked by RNA motifs. We identified the pk-turn, a new RNA motif related to k-turns that allow for the formation of a bend of 60° between stems P16 and P17 from the bacterial RNaseP. Yet it features different sequence and structural requirements than k-turns. The 2nd ribozyme which got my attention is the LCrz inserted in GIR2, a group I intron. This twintron is observed in the pre-rRNA 18S of the small subunit of the eukaryoteD. iris. LCrz catalyzes a reaction equivalent to the first step of splicing by group II introns, but in a structural context related to group I introns. We solved the 2.5 Å crystal structure of the LCrz and confirmed the unexpected shape by means of SAXS experiments. This work emphasizes the relationship between structure and function in the evolution of ribozymes.

Made available in DSpace on 2014-10-09T12:41:56Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:04:33Z (GMT). No. of bitstreams: 0 / O Laboratório de Metrologia Nuclear (LMN) do Instituto de Pesquisas Energéticas e Nucleares (IPEN) desenvolveu recentemente o Sistema de Coincidência por Software (SCS), para a digitalização e registro dos sinais de seus sistemas de coincidências 4πβ-γ utilizados na padronização de radionuclídeos. O sistema SCS possui quatro entradas analógicas independentes que possibilitam o registro simultâneo dos sinais de até quatro detectores (vias β e γ). A análise dos dados é realizada a posteriori, por software, incluindo discriminação de amplitudes, simulação do tempo-morto da medida e definição do tempo de resolução de coincidências. O software então instalado junto ao SCS estabeleceu a metodologia básica de análise, aplicável a radionuclídeos com decaimento simples, como o 60Co. O presente trabalho amplia a metodologia de análise de dados obtidos com o SCS, de modo a possibilitar o uso de detectores com alta resolução em energia (HPGe), para padronização de radionuclídeos com decaimentos mais complexos, com diferentes ramos de decaimento ou com transições metaestáveis. A expansão metodológica tem suporte na elaboração do programa de análise denominado Coincidence Analyzing Task (CAT). A seção de aplicação inclui as padronizações do 152Eu (diferentes ramos de decaimento) e do 67Ga (nível metaestável). A padronização do 152Eu utilizou uma amostra de uma comparação internacional promovida pelo BIPM (Bureau International des Poids et Mesures), podendo-se comparar a atividade obtida com o valores de laboratórios mundialmente reconhecidos, de modo a avaliar e validar a metodologia desenvolvida. Para o 67Ga, foram obtidas: a meia-vida do nível metaestável de 93 keV, por três diferentes técnicas de análise do conjunto de dados (βpronto-γatrasado-HPGe, βpronto-γatrasado-NaI e βpronto- βatrasado); as atividades de cinco amostras, normalizadas por Monte Carlo e as probabilidades de emissão gama por decaimento, para nove transições. / Tese (Doutoramento) / IPEN/T / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2017-09-20T18:06:53Z No. of bitstreams: 2 Dissertação - Bruna Luiza de Faria Rezende- 2017.pdf: 1376216 bytes, checksum: 9c03a69f7f93de81123e21bc0a3a36da (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-09-21T10:52:16Z (GMT) No. of bitstreams: 2 Dissertação - Bruna Luiza de Faria Rezende- 2017.pdf: 1376216 bytes, checksum: 9c03a69f7f93de81123e21bc0a3a36da (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-09-21T10:52:16Z (GMT). No. of bitstreams: 2 Dissertação - Bruna Luiza de Faria Rezende- 2017.pdf: 1376216 bytes, checksum: 9c03a69f7f93de81123e21bc0a3a36da (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-08-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In this work a basic immigration process was investigated which starts with a single colony with a single individual at the origin of a homogeneous tree with the other empty vertices. The process colonies are established at the vertices of the graph and each one grows during a random time, according to a process of general counting until a disaster that annihilates part of the population occurs. After the collapse a random amount of individuals survives and attempts to establish, in a independent manner, new colonies in a neighboring vertices. After a time these formed colonies also suffer catastrophes and the process is repeated. It is important to emphasize that the time until the disaster of each colony is independent of the others. Here this general process was studied under two methods, Poisson growth with geometric catastrophe and Yule growth with binomial catastrophe. That is, in each colony the population grows following a Poisson (or Yule), process during a random time, considered here exponential, and soon after that time its size is reduced according to the geometric (or binomial) law. Conditions were analyzed in the set of parameters so that these processes survived and limits were established that were relevant for the probability of survival, the number of colonies generated during the process and the range of the colonies in relation to the initial point. / Neste trabalho foi investigado um processo básico de imigração o qual é iniciado com uma única colônia com um único indivíduo na origem de uma árvore homogênea com os demais vértices vazios. As colônias do processo se estabelecem nos vértices do grafo e cada uma cresce durante um tempo aleatório, de acordo com um processo de contagem geral até ocorrer um desastre que aniquila parte da população. Após o colapso uma quantidade aleatória de indivíduos sobrevive e tenta estabelecer, de forma independente, novas colônias em vértices vizinhos. Depois de um tempo essas colônias formadas também sofrem catástrofes e o processo se repete. É importante enfatizar que o tempo até o desastre de cada colônia independe do das demais. Aqui esse processo geral foi estudado sujeito a dois métodos, crescimento de Poisson com catástrofe geométrica e crescimento de Yule com catástrofe binomial. Ou seja, em cada colônia a população cresce seguindo um processo de Poisson (ou Yule), durante um tempo aleatório, considerado aqui exponencial, e logo após esse tempo seu tamanho é reduzido de acordo com a lei geométrica (ou binomial). Foram analisadas condições no conjunto de parâmetros para que esses processos sobrevivam e foram estabelecidos limites relevantes para a probabilidade de sobrevivência, o número de colônias geradas durante o processo e o alcance das colônias em relação ao ponto inicial.