No tecido muscular esquelético, a interface entre o sarcolema e a matriz extracelular é constituída por proteínas especializadas responsáveis pela transmissão de força transversal e longitudinal à miofibra. As adaptações do músculo esquelético às forças fisiológicas e patológicas, como a imobilização segmentar e exercícios de reabilitação, podem contribuir para a percepção celular dos sinais mecânicos e, consequentemente, induzir modificações na flexibilidade e na força muscular. Este estudo investigou as respostas teciduais do músculo sóleo de ratas submetido ao estresse longitudinal induzido pela associação do treinamento do tipo alongamento passivo com a livre movimentação pós-imobilização dos membros posteriores direitos. O membro posterior direito das ratas foi imobilizado por 10 dias em flexão plantar, a fim de manter o músculo sóleo em posição de encurtamento. Após a imobilização, os animais passaram por um período de alongamento passivo manual intermitente. Antes da imobilização e durante o período de alongamento e de livre movimentação, foi realizada análise funcional da marcha dos animais. Noventa e seis ratas Wistar adultas foram divididas em 8 grupos: Imobilizado (I); Imobilizado e alongado por 1 dia (IAL(1)); Imobilizado e alongado por 3 dias (IAL(3)); Imobilizado e alongado por 10 dias (IAL(10)); Imobilizado e livre por 1 dia (IL(1)); Imobilizado e livre por 3 dias (IL(3)); Imobilizado e livre por 10 dias (IL(10)); Controle do Imobilizado (C(Imob)). Após os procedimentos experimentais, o músculo sóleo foi removido e congelado, para o processamento de reação de coloração Hematoxilina-Eosina; imunoistoquímica para fibronectina, colágenos tipos I e III; imunofluorescência de laminina, distrofina e macrófagos; western blot de laminina e distrofina. Análises qualitativa e quantitativa em Microscópio de Luz e sistema de análise de imagens foram realizadas. As variáveis foram avaliadas inter- e intra-grupos pelo Modelo de Regressão Linear com Efeitos Mistos. Após a imobilização, os animais apresentaram perda de peso corporal e alterações no tamanho e formato das fibras. Ainda, a hipocinesia modificou as variáveis funcionais da marcha, reduziu a amplitude de movimento (ADM) de dorsiflexão, aumentou a relação fibras com fibronectina intracelular/número total de fibras (rFFI/NTF), a expressão de distrofina, de laminina e dos colágenos tipos I e III. Após três dias de remobilização, as alterações morfológicas estavam exacerbadas: intensa celularidade, núcleos centralizados, corpos de inclusão, necrose. Estes achados foram mais intensos no IAL(3). Os grupos IAL(3) e IL(3) também apresentaram comprometimento funcional, restrição de ADM, aumento da rFFI/NTF e da expressão do colágeno tipo III. Outros achados observados nestes grupos foram aumento da quantidade de macrófagos no tecido e de distrofina. As anormalidades relativas aos parâmetros da marcha e as alterações morfológicas geradas pela imobilização mostraram melhora no grupo IAL(10). A remobilização associada ao alongamento durante dez dias mostrou significativa efetividade na reversão das anormalidades musculoesqueléticas induzidas pelo desuso, especialmente nas variáveis funcionais. / The interface between sarcolemma and extracellular matrix in skeletal muscle tissue is constituted by specialized proteins that are responsible for the transversal and longitudinal forces transmission to the myofiber. Skeletal muscle adaptations to physiological and pathological forces, such as segmental immobilization and rehabilitation exercises, may contribute to cellular perception of mechanical signals and consequently induce alterations related to flexibility and muscular force. This study investigated the tissue responses of the soleus muscle in female rats caused by longitudinal stress induced by the association of passive stretching training with the free movement after immobilization of the right hind limb. The right hind limbs of female rats were immobilized during 10 days in a plantar flexion in order to keep the soleus muscle in a shortened position. After the immobilization, the animals were submitted to intermittent passive manual stretching. The animals gait was functionally analyzed before immobilization and during the period of stretching or free movement. Ninety-six adult female Wistar rats were divided into 8 groups: Immobilized (I); Immobilized and stretched for 1 day (IS(1)); Immobilized and stretched for 3 days (IS(3)); Immobilized and stretched for 10 days (IS(10)); Immobilized and free for 1 day (IF(1)); Immobilized and free for 3 days (IF(3)); Immobilized and free for 10 days (IF(10)); Immobilized control (C(Immob)). After the experimental period, the soleus muscle was removed, frozen and further processed by Hematoxylin-eosin stain; immunohistochemistry reactions for fibronectin, types I and III collagen; imunofluorescence of laminin, dystrophin and macrophages; western blot of dystrophin and laminin. Qualitative and quantitative results were obtained using a Light Microscope and a system of image analysis. The between- and within-group data were analyzed using Mixed-Effects Linear Models. After the immobilization, the animals presented loss of body weight and alterations in size and shape of the fibers. Furthermore, the hypokinesia changed the functional variables of gait, reduced the dorsiflexion range of motion (ROM), increased the intracellular fibronectin/total number of fibers ratio (FIF/TNFr), the expression of dystrophin, of laminin and of the types I and III collagen. After three days of remobilization, the morphological changes were exacerbated: intense cellularity, nuclear centralization, inclusion bodies and necrosis. These findings showed increased in the IS(3). The groups IS(3) and IF(3) also showed functional impairment, ROM restriction, increased FIF/TNFr and immunoreactivity of the type III collagen. Others findings observed in these groups were increase of the amount of macrophages in the tissue and of dystrophin. The abnormalities related to gait parameters and the morphological changes induced by immobilization were improved in the IS(10) group. The remobilization using stretching for ten days showed significant effectiveness and reverted the skeletal muscle abnormalities induced by disuse, especially concerning the functional variables.

Orientadores: Daniela Mariz Silva Vieira, Jorge Tulio Mujica Ascui / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Matemática, Estatística e Computação Científica / Made available in DSpace on 2018-08-19T00:22:09Z (GMT). No. of bitstreams: 1 Nachtigall_Cicero_D.pdf: 625263 bytes, checksum: 7dc27b9956ffbb6e717aa95776b7b8c8 (MD5) Previous issue date: 2011 / Resumo: O resumo, na íntegra, poderá ser visualizado no texto completo da tese digital. / Abstract: The complete abstract is available with the full electronic digital thesis or dissertations. / Doutorado / Matematica / Doutor em Matemática

La thèse contribue à une meilleure connaissance du processus d’éco-conception de produits, notamment dans la prise en compte de considérations environnementales en amont du processus de conception. Centrée sur la phase conceptuelle, la motivation principale de ce travail est d’intervenir là où les décisions du concepteur ont une grande influence environnementale. En effet, un grand nombre d’auteurs convient que les premières étapes du processus de conception peuvent efficacement prévenir jusqu’à 80% des impacts environnementaux. Cependant, il existe un grand nombre d’obstacles qui empêchent l’intégration de considérations environnementales, surtout s’il s’agit d’un nouveau produit. Notre problématique a mis en évidence ces obstacles à travers deux types de verrous. En premier lieu, des verrous méthodologiques rencontrés principalement lors de la phase conceptuelle. En deuxième lieu, des verrous opérationnels liés au manque de connaissances environnementales du concepteur. En réponse à ces verrous nous proposons la création de liens entre l’analyse de cycle de vie (ACV) et l’analyse fonctionnelle (AF). Ces liens donnent lieu à un processus collaboratif d’éco-conception qui est en partie supporté par la méthode EcoAF spécialement développée à cet effet. La méthode intègre le concept de cycle de vie de l’ACV lors de la réalisation de l’AF, permettant ainsi de guider le concepteur vers l’intégration de considérations environnementales pour la création d’un produit avec un rendement environnemental équilibré sur l’ensemble du cycle de vie / The thesis contributes to a better understanding of the eco-design process of products, especially in the integration of environmental considerations in the early phases of the design process. Focused on the conceptual phase, the main motivation of this work is to intervene when the decisions of the designer have the greatest environmental influence. Indeed, many authors agree that the early stages of the design process can prevent up to 80% of environmental impacts. However, there are also many obstacles to the integration of environmental considerations, especially for a new product. The obstacles are highlighted through two types of locks. First, methodological locks encountered mainly at the conceptual stage. Secondly, operational locks are related with the lack of environmental knowledge of the designer. To solve the problems, we propose the creation of links between the life-cycle assessment (LCA), method that includes environmental knowledge, and functional analysis (FA), method well known by the designer early in the design process. These links have resulted in a collaborative eco-design process that is partly supported by the creation of the EcoAF method. Eco AF integrates life cycle concept of LCA when performing AF. It makes it possible to guide the designer in the integration of environmental considerations in creating a product with a balanced environmental performance throughout the life cycle

La dégradation des ARN messagers (ARNm) est un processus universel extrêmement complexe. D’une manière semblable aux polymerases pour la transcription et ribosomes pour la traduction, les complexes de protéines effectuant la dégradation des ARNm sont précisément régulés. La dégradation des ARNm eucaryotes s’effectue selon un schéma conservé évolutivement qui est initié par la déadénylation résultant dans la formation de transcrits avec des queues polyA courtes. De tels intermédiaires sont alors dégradés par le clivage de leur coiffe suivi par une digestion exonucléolytique 5’-3’ effectuée par Xrn1, ou alternativement par une digestion 3 ’-5’ catalysée par l’exosome. Dans ma thèse je présente une dissection fonctionnelle du complexe de déadénylation CCR4-NOT basée sur son analyse structurale. Je me suis essentiellement intéressé à cinq questions fondamentales concernant ce complexe : La formation du complexe CCR4-NOT complexe est-elle requise pour la déadénylation ? Quel est le rôle moléculaire de sous-unités Not2/3/5 du complexe ? Pourquoi la protéine Not1 est-elle essentielle chez la levure ? Le complexe CCR4-NOT joue-t-il un rôle dans la répression de la traduction ? Comment le complexe CCR4-NOT est-il ciblé sur ses substrats ARNm ? / MRNA degradation is a highly complex and versatile process. In a manner similar to polymerase complexes in transcription and ribosomes in translation, protein complexes mediating mRNA decay are tightly regulated. Eukaryotic mRNA decay follows a conserved pathway initiated by deadenylation that generates transcripts with short polyA tails. The latter intermediates are degraded either by decapping followed with 5’-3’ trimming mediated by Xrn1, or by exosome-mediated digestion in the 3’-5’ direction. In my thesis I present a functional dissection of the Ccr4-Not deadenylase complex based on its structural analysis. Essentially, I addressed five fundamental questions related to this complex: Is CCR4-NOT complex formation required for deadenylation activity? What is the molecular role of associated Not2/3/5 subunits? Why is the Not1 protein essential in yeast? Does the CCR4-NOT complex play role in translation regulation? How is the CCR4-NOT complex targeted to its mRNA substrates?

Les couvertures d'infrastructure de transport en milieu urbain sont des opérations urbaines répondant à un certain nombre de problématiques de politique publique relatives à des questions urbaines, foncières, etc. Elles s'attachent notamment à la résorption et au traitement de l'effet de coupure et autres nuisances générées par la présence de grand linéaires routiers ou ferroviaires au sein d'un tissu urbain dense. Ces interventions, résolument complexes, souffrent de l'absence de cadre spécifique et d'un manque de vision globale.Afin de proposer des méthodes et des outils d'évaluation des couvertures d'infrastructures en milieu urbain aux acteurs concernés par ces projets, ce travail de doctorat élabore une méthode fondée sur une approche systémique. La modélisation fonctionnelle permet d'intégrer la complexité que représente le système couverture d'infrastructure dans son contexte urbain et de formaliser les interactions caractérisant le système, les hiérarchiser et y associer des méthodes d'évaluations. Le travail de modélisation, dans sa phase de validation, est mené sur plusieurs couvertures, concernant des typologies d'infrastructures différentes et de contextes urbains contrastés. Des perspectives d'évaluation sont alors envisagées sur la base du modèle fonctionnel obtenu. / Structural covers for transport infrastructures in an urban environment answer to public policy issues relating to urban questions, real estate questions, etc. They adress in particular the absorption and processing of the barrier effect and other nuisances generated by the presence of large road or rail linear within a dense urban fabric. These interventions, resolutely complexes, suffer from the absence of a specific framework and a lack of overall global vision.In order to propose methods and tools for urban structural cover assessment to the actors affected by these projects, this PhD work thesis develops a method based on a systemic approach. Functional modeling allows to integrate the complexity that represents the system infrastructure cover in its urban context, and to formalize the interactions that characterize the system, to prioritize them and to associate them evaluation methods. The modeling work in its validation phase is conducted on several structural covers, concerning different infrastructure types and contrasting urban contexts. Some perspectives of assessment are considered, based on the obtained functional model.

Bipolar disorder and schizophrenia are two severe psychiatric disorders characterized by a complex genetic basis, coupled to the influence of environmental factors. In this thesis, functional genomic analysis tools were used for the study of the underlying pathophysiology of these disorders, focusing on gene expression and function on a global scale with the application of high-throughput methods. Datasets from public databases regarding transcriptomic data of postmortem brain and skin fibroblast cells of patients with either schizophrenia or bipolar disorder were analyzed in order to identify differentially expressed genes. In addition, fibroblast cells of bipolar disorder patients obtained from the Biobank of the Neuropsychiatric Research Laboratory of Örebro University were cultured, RNA was extracted and used for microarray analysis. In order to gain deeper insight into the biological mechanisms related to the studied psychiatric disorders, the differentially expressed gene lists were subjected to pathway and target prioritization analysis, using proprietary tools developed by the group of Metabolic Engineering and Bioinformatics, of the National Hellenic Research Foundation, thus indicating various cellular processes as significantly altered. Many of the molecular processes derived from the analysis of the postmortem brain data of schizophrenia and bipolar disorder were also identified in the skin fibroblast cells. Additionally, through the use of machine learning methods, gene expression data from patients with schizophrenia were exploited for the identification of a subset of genes with discriminative ability between schizophrenia and healthy control subjects. Interestingly, a set of genes with high separating efficiency was derived from fibroblast gene expression profiling. This thesis suggests the suitability of skin fibroblasts as a reliable model for the diagnostic evaluation of psychiatric disorders and schizophrenia in particular, through the construction of promising machine-learning based classification models, exploiting gene expression data from peripheral tissues.

Please read the abstract in the section 00front of this document / Dissertation (MSc (Industrial Systems))--University of Pretoria, 2006. / Industrial and Systems Engineering / unrestricted

La pyriculariose provoquée par le champignon Magnaporthe oryzae constitue l’une des principales maladies du riz, avec des épidémies récurrentes et très destructrices qui touchent toutes les régions rizicoles. Outre les enjeux économiques et humanitaires liés à cette maladie, le statut de céréale modèle du riz et de champignon parasite modèle de M. oryzae font de l’interaction entre ces deux partenaires un modèle privilégié pour l’étude du contrôle génétique et moléculaire des relations hôte-pathogène. Les protéines effectrices, Avr, de M. oryzae sont sécrétées au cours de l’infection de la plante par ce champignon. Chez certaines variétés de riz ces effecteurs agissent comme des protéines d’avirulence. Elles sont reconnues par les protéines de résistance, R, et induisent une forte réponse de défense dont une mort cellulaire programmée appelée HR (hypersensitive response) à l’origine de la résistance de la plante. L’objectif de cette thèse est de déterminer les structures des protéines Avr, et R et celles des complexes Avr-R. L'analyse structure-fonction permettra d’identifier les domaines et les acides aminés importants pour l'activité des effecteurs et des protéines de résistance. Pour la réalisation de cette thèse, une large gamme de techniques de biologie moléculaire (PCR, clonage moléculaire), de biophysique (Fluorescence) et de biologie structurale (RMN, cristallographie aux RX) disponibles au laboratoire seront utilisées. Du point de vue fonctionnel, ces études devraient apporter de nouveaux éléments sur les fonctions végétales qui sont modulées au cours de l’infection et permettent ainsi à la maladie de s'établir en créant des conditions favorables à la mise en place du processus infectieux. / MAGNAPORTHE oryzae causes a devastating disease of rice known as rice blast, affecting all regions cultivating rice. In addition to the economic and humanitarian issues associated with the disease, rice and M. oryzae are widely accepted as models of cereal and fungus for studying genetic control and host-pathogen molecular interactions. The effector proteins, Avr of M. oryzae, are secreted during plant infection by the fungus. In some of the rice cultivation these effectors act as avirulence proteins. They are recognized by resistance proteins R, and induce a strong host response, including programmed cell death known as HR (hypersensitive response) leading to plant resistance. The purpose of the thesis is to elucidate the atomic structures of the proteins Avr, R and Avr-R complexes. Subsequent structure-function analysis will identify domains and important amino acids needed for the activity of the effector and resistance proteins. To carry out this thesis, a wide range of molecular biology techniques (pcr, molecular cloning), biophysics (fluorescence) and structural biology (NMR, X-ray crystallography) will be used. From the functional point of view, these studies will provide insight into mechanisms affecting host functions that are modulated during infection, thus creating favorable conditions for the infection process.

Mucosa associated lymphoid tissue (MALT) lymphoma is characterized by t(11;18)(q21;q21)/API2-MALT1, t(1;14)(p22;q32)/BCL10-IGH andt(14;18)(q32;q21)/IGH-MALT1, which commonly activate the NF-κB pathway. Gastric MALT lymphomas harbouring such translocation do not respond to Helicobacter pylori eradication, while those without translocation can be cured by antibiotics. To understand the molecular mechanism of MALT lymphoma with and without chromosome translocation, 24 cases (15 translocation-positive and 9 translocation-negative) of MALT lymphomas together with 7 follicular lymphomas and 7 mantle cell lymphomas were analysed by Affymetrix gene expression microarray platform. Unsupervised clustering showed that cases of MALT lymphoma were clustered as a single branch. However, within the MALT lymphoma group, translocation-positive cases were intermingled with translocation-negative cases. Gene set enrichment analysis (GSEA) of the NF-κB target genes and 4394 additional gene sets covering various cellular pathways, biological processes and molecular functions showed that translocation-positive MALT lymphomas were characterized by an enhanced expression of NF-κB target genes, particularly TLR6, CCR2, CD69 and BCL2, while translocation-negative cases were featured by active inflammatory and immune responses, such as IL8, CD86, CD28 and ICOS. Separate analyses of the genes differentially expressed between translocation-positive and negative cases and measurement of gene ontology term in these differentially expressed genes by hypergeometric test reinforced the above findings by GSEA. The differential expression of these NF-κB target genes between MALT lymphoma with and without translocation was confirmed by quantitative RT-PCR and immunohistochemistry or Western blot. Expression of TLR6, in the presence of TLR2, enhanced both API2-MALT1 and BCL10 mediated NF-κB activation in vitro. In addition, there was cooperation between expression of BCL10, MALT1 or API2-MALT1, and stimulation of the antigen receptor or CD40 or TLR in NF-κB activation as shown by both reporter assay and IκBα degradation. Interestingly, expression of BCL10 but not API2-MALT1 and MALT1, in the presence of LPS stimulation, also triggered IκBβ degradation, suggesting activation of different NF-κB dimers between these oncogenic products. Study by co-immunoprecipitation showed that BCL10 directly interacts with MALT1. Sub-cellular localisation experiments in BJAB B-cells, showed that BCL10 localisation was affected by MALT1. When BCL10 was over-expressed, the protein was predominantly expressed in the nuclei, but when MALT1 was over-expressed, BCL10 was mainly localised in the cytoplasm. When both BCL10 and MALT1 were over-expressed, BCL10 was expressed in the cytoplasm in the early hours when the protein level was low, but in both the cytoplasm and nuclei after 9 hours when the protein level was high. Over-expression of API2-MALT1 did not shown any apparent effect on BCL10 sub-cellular localisation in vitro. Finally, comparison of MALT lymphoma expression microarray with other lymphomas showed lactoferrin to be highly expressed in MALT lymphoma. This was confirmed by qRT-PCR, showing lactoferrin to be significantly over-expressed in MALT lymphoma compared to FL and MCL. Thus lactoferrin may be a potential marker for MALT lymphoma.

A pair of commuting bounded operators (S, P) for which the set r = {(z 1 +z 2,z 1z 2) : |z 1| ≤1, |z 2| ≤1} C2 is a spectral set, is called a r-contraction in the literature. For a contraction P and a bounded commutant S of P, we seek a solution of the operator equation S –S*P = (I –P*P)½ X(I –P*P)½ where X is a bounded operator on Ran(I – P*P)½ with numerical radius of X being not greater than 1. We show the existence and uniqueness of solution to the operator equation above when (S,P) is a r-contraction. We call the unique solution, the fundamental operator of the r-contraction (S,P). As the title indicates, there are three parts of this thesis and the main role in all three parts is played by the fundamental operator. The existence of the fundamental operator allows us to explicitly construct a r-isometric dilation of a r-contraction (S,P), whereas its uniqueness guarantees the uniqueness of the minimal r-isometric dilation. The fundamental operator helps us to produce a genuine functional model for pure r-contractions. Also it leads us to a complete unitary invariant for pure r-contractions. We decipher the structures of r-isometries and r-unitaries by characterizing them in several different ways. We establish the fact that for every pure r-contraction (S,P), there is a bounded operator C with numerical radius being not greater than 1 such that S = C + C* P. When (S,P) is a r-isometry, S has the same form where P is an isometry commuting with C and C*. Also when (S,P) is a r-unitary, S has the same form too with P and C being commuting unitaries. Examples of r-contractions on reproducing kernel Hilbert spaces and their dilations are discussed.