A qualidade do ambiente das áreas destinadas às florestas é afetada pelos problemas de compactação do solo devido a causas naturais e induzidas pelo tráfego de veículos. O objetivo deste trabalho foi definir as prioridades do preparo mecanizado do solo a partir das exigências das mudas de Eucalyptus spp. A execução do trabalho foi realizada entre dezembro de 2000 a maio de 2001, na Companhia Suzano de Papel e Celulose, município de São Miguel Arcanjo (S.P). O método utilizado teve duas fases: Planejamento da Qualidade, e Avaliação da Qualidade. A primeira fase, consistiu em sistematizar o conceito emitido, por uma equipe especializada na produção florestal, sobre a qualidade do preparo mecanizado do solo para mudas de Eucalyptus spp, utilizando-se do Desdobramento da Função Qualidade (QFD), e a segunda fase, Avaliação da Qualidade, consistiu em verificar as prioridades técnicas através de histograma e carta de controle. Os resultados evidenciaram que os itens da qualidade exigida não possuir limitações físicas, e sem restevas que limitem a mecanização tem respectivamente 19,4% e 15,0% de peso relativo. O requisito técnico profundidade do sulco de plantio relacionou-se fortemente com os itens da qualidade exigida, e apresentou 25,7% de peso relativo. Também, o indicador profundidade do sulco, correlacionou-se fortemente com a largura do sulco e com o tamanho dos torrões, cujos pesos relativos foram iguais a 26,4% e 23,0%. Os fatores operacionais do preparo mecanizado do solo, regulagens do sulcador/implemento e a distribuição da resteva superficial, apresentaram respectivamente 25,6% e 64,0% de pesos relativos, e os graus do custo econômico destes fatores foram respectivamente 1 e 5. As conclusões da pesquisa foram: os itens da qualidade exigida não possuir limitações físicas, e sem restevas que limitem a mecanização são prioritários para as mudas de Eucalyptus spp, sendo que a prioridade técnica foi a profundidade do sulco, tornando-se o indicador da qualidade do preparo mecanizado do solo, o qual será controlado através das regulagens do sulcador/implemento. Nas faixas de galhada, o controle da profundidade do sulco será determinado pela distribuição da resteva superficial. / The quality of the environment of areas destined to artificial forest is reduced by the problems of soil compactation due to natural causes and induced by the traffic of vehicles. The aim of this work was to define the priorities of the mechanized preparation of the soil based on the demands of the Eucalyptus spp seedlings. The work was done during December 2000 to May 2001 at Companhia Suzano de Papel e Celulose, S.P. The method used had two steps: planning of the quality and evaluation of the quality. The first stage consisted of systematizing the concepts about soil preparation emitted by a team of experts in forest production using the Quality Function Deployment (QFD). The second stage, evaluation of the quality, consisted in checking the technical priorities in an experimental area. The results were analized using statistical quality tools mainly histograms and control charts. The results showed that the itens of the demanded quality, not having the physical limitation and without residue that limit the mechanization, have 19.4% and 15.0% respectively of relative weight. The technical requirement, depth of the planting furrow, was strongly related with the itens of demanded quality and it represents 27.5% of relative weight. Also the indicator depth of furrow, was strongly conected with the furrow width and size of soil lumps which the relative weights were 26.4% and 23.0% respectively. The operational factors of soil mechanization, subsoiler adjust and the distribution of the superficial residue, showed respectively 25.6% and 64.0% of the relative weights and the degrees of economical cost of these factors were classified as 1 and 5. The conclusions of the work were: the itens of the demanded quality, not having the physical limitation and without residue that limit the mechanization, are priority for the plants of Eucalyptus; the technical requirement, depth of the planting furrow, becoming the indicator of quality of the soil preparation and it will be controlled through the subsoiler adjustment; in the strips of the wood debris the depth control will be determined by the distribution of the superficial residue.

A qualidade do ambiente das áreas destinadas às florestas é afetada pelos problemas de compactação do solo devido a causas naturais e induzidas pelo tráfego de veículos. O objetivo deste trabalho foi definir as prioridades do preparo mecanizado do solo a partir das exigências das mudas de Eucalyptus spp. A execução do trabalho foi realizada entre dezembro de 2000 a maio de 2001, na Companhia Suzano de Papel e Celulose, município de São Miguel Arcanjo (S.P). O método utilizado teve duas fases: Planejamento da Qualidade, e Avaliação da Qualidade. A primeira fase, consistiu em sistematizar o conceito emitido, por uma equipe especializada na produção florestal, sobre a qualidade do preparo mecanizado do solo para mudas de Eucalyptus spp, utilizando-se do Desdobramento da Função Qualidade (QFD), e a segunda fase, Avaliação da Qualidade, consistiu em verificar as prioridades técnicas através de histograma e carta de controle. Os resultados evidenciaram que os itens da qualidade exigida não possuir limitações físicas, e sem restevas que limitem a mecanização tem respectivamente 19,4% e 15,0% de peso relativo. O requisito técnico profundidade do sulco de plantio relacionou-se fortemente com os itens da qualidade exigida, e apresentou 25,7% de peso relativo. Também, o indicador profundidade do sulco, correlacionou-se fortemente com a largura do sulco e com o tamanho dos torrões, cujos pesos relativos foram iguais a 26,4% e 23,0%. Os fatores operacionais do preparo mecanizado do solo, regulagens do sulcador/implemento e a distribuição da resteva superficial, apresentaram respectivamente 25,6% e 64,0% de pesos relativos, e os graus do custo econômico destes fatores foram respectivamente 1 e 5. As conclusões da pesquisa foram: os itens da qualidade exigida não possuir limitações físicas, e sem restevas que limitem a mecanização são prioritários para as mudas de Eucalyptus spp, sendo que a prioridade técnica foi a profundidade do sulco, tornando-se o indicador da qualidade do preparo mecanizado do solo, o qual será controlado através das regulagens do sulcador/implemento. Nas faixas de galhada, o controle da profundidade do sulco será determinado pela distribuição da resteva superficial. / The quality of the environment of areas destined to artificial forest is reduced by the problems of soil compactation due to natural causes and induced by the traffic of vehicles. The aim of this work was to define the priorities of the mechanized preparation of the soil based on the demands of the Eucalyptus spp seedlings. The work was done during December 2000 to May 2001 at Companhia Suzano de Papel e Celulose, S.P. The method used had two steps: planning of the quality and evaluation of the quality. The first stage consisted of systematizing the concepts about soil preparation emitted by a team of experts in forest production using the Quality Function Deployment (QFD). The second stage, evaluation of the quality, consisted in checking the technical priorities in an experimental area. The results were analized using statistical quality tools mainly histograms and control charts. The results showed that the itens of the demanded quality, not having the physical limitation and without residue that limit the mechanization, have 19.4% and 15.0% respectively of relative weight. The technical requirement, depth of the planting furrow, was strongly related with the itens of demanded quality and it represents 27.5% of relative weight. Also the indicator depth of furrow, was strongly conected with the furrow width and size of soil lumps which the relative weights were 26.4% and 23.0% respectively. The operational factors of soil mechanization, subsoiler adjust and the distribution of the superficial residue, showed respectively 25.6% and 64.0% of the relative weights and the degrees of economical cost of these factors were classified as 1 and 5. The conclusions of the work were: the itens of the demanded quality, not having the physical limitation and without residue that limit the mechanization, are priority for the plants of Eucalyptus; the technical requirement, depth of the planting furrow, becoming the indicator of quality of the soil preparation and it will be controlled through the subsoiler adjustment; in the strips of the wood debris the depth control will be determined by the distribution of the superficial residue.

The major allergen Der p 1 of the house dust mite Dermatophagoides pteronyssinus is a papain-like cysteine protease (CA1) associated to the development of allergic diseases such as asthma, rhinitis or atopic dermatitis. This allergen is expressed as an inactive precursor, called proDer p 1, formed by a 25 kDa catalytic domain downstream to an 10 kDa N-terminal propeptide, which blocks the active site cleft. The propeptide of Der p 1 exhibits a specific fold, which makes it unique in the CA1 propeptide family as it is characterised by the presence of four alpha helices and the absence of ERFNIN motif. In this study, we investigated the activation steps involved in the maturation of recombinant proDer p 1 expressed in Pichia pastoris under acidic conditions and we studied the influence of acidic pH on the structure of both propeptide and catalytic domain. Therefore, we characterized the interaction between the propeptide and mature Der p 1 at different pH values in terms of activity inhibition, structural stability and proteolytic susceptibility. According to our results, the auto-activation of proDer p 1 is a multistep mechanism, characterized by at least two intermediates (ATFE- and SNGG-) corresponding to the loss of the first and second propeptide alpha helices, respectively. The propeptide strongly inhibits unglycosylated and glycosylated recombinant Der p 1 (KD= 7 nM) at neutral pH. This inhibition is pH dependent, decreasing from pH 7 to pH 4 and can be related to structural changes of the propeptide initiated by the protonation of the aspartate residue of Lys17-Asp51-Tyr19 structural triad presents within the propeptide N-terminal domain. This protonation triggers conformational changes of the first propeptide alpha helix leading to an increase of the propeptide flexibility, an increase of its proteolytic sensitivity and the formation of a molten globule state. In addition, we compare mature protease, zymogen and propeptide pH unfolding and stability and highlights that the presence of the propeptide does not influence the catalytic domain pH unfolding and stability as the propeptide displays a weaker pH stability than the protease domain. These results confirmed that the propeptide unfolding is the key event of the activation process. Finally, we unravel the intermolecular contribution of mature Der p 1 in the activation process and highlights that activation of the precursor can be achieved, under acidic conditions, by intermolecular process but initial auto-activation most probably occurs through an intramolecular process or by the proteolysis by the catalytic domain of another zymogen in which the propeptide is unfolded. According to our results, we proposed that activation of the zymogen at pH 4 reflects a compromise between activity preservation and propeptide unfolding and that the location of the activation sites on the propeptide structure is a compromise between sequence recognition specificity and proteolytic susceptibility of the corresponding area.

This thesis describes the development of electronic modules for fusion neutron spectroscopy as well as several implementations of artificial neural networks (NN) for neutron diagnostics for the Joint European Torus (JET) experimental reactor in England. The electronics projects include the development of two fast light pulser modules based on Light Emitting Diodes (LEDs) for the calibration and stability monitoring of two neutron spectrometers (MPRu and TOFOR) at JET. The particular electronic implementation of the pulsers allowed for operation of the LEDs in the nanosecond time scale, which is typically not well accessible with simpler circuits. Another electronic project consisted of the the development and implementation at JET of 32 high frequency analog signal amplifiers for MPRu. The circuit board layout adopted and the choice of components permitted to achieve bandwidth above 0.5 GHz and low distortion for a wide range of input signals. The successful and continued use of all electronic modules since 2005 until the present day is an indication of their good performance and reliability. The NN applications include pulse shape discrimination (PSD), deconvolution of experimental data and tomographic reconstruction of neutron emissivity profiles for JET. The first study showed that NN can perform neutron/gamma PSD in liquid scintillators significantly better than other conventional techniques, especially for low deposited energy in the detector. The second study demonstrated that NN can be used for statistically efficient deconvolution of neutron energy spectra, with and without parametric neutron spectroscopic models, especially in the region of low counts in the data. The work on tomography provided a simple but effective parametric model for describing neutron emissivity at JET. This was then successfully implemented with NN for fast and automatic tomographic reconstruction of the JET camera data. The fast execution time of NN, i.e. usually in the microsecond time scale, makes the NN applications presented here suitable for real-time data analysis and typically orders of magnitudes faster than other commonly used codes. The results and numerical methods described in this thesis can be applied to other diagnostic instruments and are of relevance for future fusion reactors such as ITER, currently under construction in Cadarache, France.

<p>Ankyrin repeats (ARs) are polypeptide motifs identified in thousands of proteins. Many AR proteins play a function as scaffolds in protein-protein interactions which may require specific mechanical properties. Also, a number of AR proteins have been proposed to mediate mechanotransduction in a variety of different functional settings. The folding and stability of a number of AR proteins have been studied in detail by chemical and temperature denaturation experiments, yet the mechanic of AR proteins remain largely unknown. In this dissertation, we have researched the mechanical properties of AR proteins by using protein engineering and a combination of atomic force microscopy (AFM)-based single-molecule force spectroscopy and steered molecular dynamics (SMD) simulations. Three kinds of AR proteins were investigated: NI6C (synthetic AR protein), D34 (of ankyrin-R) and gankyrin (oncoprotein). While the main focus of this research was to characterize the response of AR proteins to mechanical forces, our results extended beyond the protein nanomechanics to the understanding of protein folding mechanisms.</p> / Dissertation

For all living systems, there is a requirement to recycle and regulate proteins. In eukaryotic organisms this is accomplished by the proteasome. The p97 ATPase is another highly conserved and essential complex present throughout the eukaryotic cell. In Paper I we utilized UFD fluorescent substrates to address the role of p97 and cofactors in soluble proteasome degradation. Results using RNAi and Drosophila p97 mutants propose p97 to function upstream of the proteasome on cytosolic proteasome targets as an important unfoldase together with its Ufd1/Npl4 cofactors. The results implicate p97 to be important for degradation of proteasome substrates lacking natural extended peptide regions. In Paper II we focused on identifying transcription factors essential for production of proteasomal subunits and associated proteins in Drosophila S2 cells. We utilized an RNA library targeting 993 known or candidate transcription factors and monitored RNAi depleted Drosophila S2 cells expressing the UFD reporter UbG76VGFP. We identified a range of potential candidates and focused on the bZIP transcription factor Cnc-C. RNAi and qrt-PCR experiments implicated Cnc-C to be involved in transcription of proteasomal subunits. In Paper III we applied our knowledge gained from Paper I about p97 dependent substrates and set up a high-throughput microscopy screening method to potentially find inhibitors specifically targeting the p97 proteasomal sub-pathway. Utilizing UFD substrates with and without C-terminal peptide tails we determined if compounds inhibited the core proteasomal machinery or the p97 pathway specifically. Through a primary and secondary round of screening we identified several new compounds inhibiting the ubiquitin-proteasome pathway though none from our initial screening had specificity for p97. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.

Made available in DSpace on 2014-06-11T19:26:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-03-03Bitstream added on 2014-06-13T20:27:28Z : No. of bitstreams: 1 bronzi_ma_me_sjrp.pdf: 904425 bytes, checksum: 2344eb35a112034c2f1741b2e229f1ec (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Estudamos intersecções homoclínicas de variedades estável e instável de pontos peródicos. Toda intersecção homoclínica produz um comportamento curioso na dinâmiôa. Nosso modelo de tal fenômeno é a famosa ferradura de Smale, a qual é um conjunto hiperbólico para um difeomorfismo. Além disso, estudamos dinâmica não hiperbólica cuja perda de hiperbolicidade é divido à tangências homoclínicas. Elas tem um papel central na teoria de sistemas dinâmicos. O desdobramento de uma tangência homoclínica produz dinâmicas muito interessantes. Neste trabalho estudamos a criação de cascatas de bifurcações de duplicação de período e um esquema de renormalização para uma tangência homoclínica. / We study homoclinic intersection of stable and unstable manifolds of periodic points. Every homoclinic intersection produce a intricate behavior of the dynamics. Our model of such phenomena is the so called Smalesþs horseshoe, which is a hyperbolic set for a di eomorphism. We also study non hyperbolic dynamics whose lack of hyperbolicity is due to homoclinic tangencies. They play a central role in the theory of dynamical systems. The unfolding of a homoclinic tangency produce many interesting dynamics. In this work we study creation of cascade of period doubling bifurcations and a renormalization scheme for a homoclinic tangency.

La polarisation du quark top produit par interaction électrofaible (single-top) en voie-t permet de tester la structure du vertex Wtb: le couplage vecteur gauche prévu dans le cadre du Modèle Standard (MS), ainsi que les couplages anormaux vecteur ou tenseur introduits par plusieurs théories au-delà du Modèle Standard. Le lot de données correspondant à une luminosité integrée de 4,7 fb-1 recolté dans les collisions proton-proton à une énergie de 7 TeV dans le centre de masse offre une chance de mesurer la polarisation du quark top. Cette thèse traite de la mesure de la polarisation du quark top grâce à l'étude des distributions angulaires polarisées dans des bases spécifiques avec les événements single-top produits en voie-t. Au début du document, le contexte théorique de production du quark top par interaction forte et électrofaible au LHC est introduit. Ensuite, le détecteur, les performances de reconstruction ainsi que la sélection d'événements avec une signature single-top en voie-t, sont décrits. Les méthodes d' "unfolding" et de "folding" sont présentées et testées avec différentes configurations afin de mesurer la polarisation du quark top. Les résultats obtenus, ainsi que les incertitudes théorique, expérimentales et statistiques, sont examinées. Il s'agit de la première mesure de polarisation du quark top avec le détecteur ATLAS. Les résultats sont compatibles avec les prédictions MS, et contribuent donc à contraindre de maniére significative les couplages anormaux sur le vertex Wtb. / The top quark polarization in electroweak production for single top t-channel allows to test the structure of the Wtb vertex: the left-handed vector coupling of the Standard Model (SM) as well as the anomalous couplings including the right-handed vector, the left-handed tensor and the right-handed tensor couplings. The 4.7 fb-1 data recorded by the ATLAS detector at the LHC with the center of mass energy at 7 TeV in 2011 provides a chance to measure the top polarization. This thesis discusses the measurement of the top polarization by studying the polarized angular distributions in specific bases with t-channel single top events. In the beginning of the thesis, a theoretical context of the top quark production via the strong interaction and the electroweak interaction at the LHC is introduced. Then the detector, the reconstruction performances as well as the event selections with a single top t-channel event signature are described. To measure the top polarization, the unfolding and folding methods are constructed and tested with different configurations. In the end, the measured results are examined with the estimated uncertainties from the theory, the detector response and modeling as well as the statistics. This is the first measurement of the top polarization with the ATLAS detector. The results are compatible with the SM predictions and contribute signicantly to constrain the anomalous couplings in the Wtb vertex

Ce travail de thèse ce concentre sur l’étude des protéines par l’usage de haute pression. Les articles présentés ici sont précéder d’une introduction présentant les différents modèles physiques utilisés pour décrire le repliement des protéines, une introduction posant les bases de la thermodynamique, ainsi que l’origine de la stabilité thermodynamique des protéines dans leur état plies. Il y a trois sujets principaux aborder dans ce mémoire. Le premier est l’étude de la coopérativité du repliement et du paysage de repliement de la protéine à répétition PP32 (Anp32a) a travers l’utilisation de la pression a différentes températures. La seconde étude concerne l’investigation de l’origine de l’expansivité thermique des protéines pliées grâce à l’utilisation de RMN haute pression et de la protéine très bien caractérisée Staphylococcal Nuclease (SNase) et de certaine de ses mutantes. Finalement, un dernier article sur la stabilité sous pression de la variant TC5b de la mini protéine model tryptophan-cage grâce une combinaison de RMN et de simulations moléculaires tout-atomes en « replica exchange ». / This thesis work focuses on the study of protein though the use of high pressure. There are three main points subject that are being inquired here. The first is the study of cooperativity and folding landscape of a repeat protein (Anp32a) though the use high pressure denaturation at different temperatures. The second concerns the investigation of the determinant of thermal expansivity in the folded state of protein using high pressure NMR, and the well characterized Staphylococcal Nuclease (SNase) and some of its mutants. Finally, a last article on the pressure stability of the model mini protein Tryptophan cage variant Tc5b by a combination of high pressure NMR and full atomic replica exchange simulations.

Made available in DSpace on 2014-06-11T19:22:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-07-17Bitstream added on 2014-06-13T20:08:00Z : No. of bitstreams: 1 goncalves_er_me_sjrp_parcial.pdf: 124608 bytes, checksum: 0a4bcc296ede029511807eb42a3bd883 (MD5) Bitstreams deleted on 2014-08-22T14:57:05Z: goncalves_er_me_sjrp_parcial.pdf,Bitstream added on 2014-08-22T15:02:08Z : No. of bitstreams: 1 000607885.pdf: 2203958 bytes, checksum: 2ad68620c13ca42941cc766689b448fd (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Este trabalho apresenta um estudo do processo de desenovelamento da papaína via temperatura. Para tanto, foi utilizada a técnica espectroscópica de fluorescência, em conjunto com a espectroscopia de correlação bidimensional, com as análises sample-sample e variável- variável aplicadas à região do infravermelho médio. Desta forma, foi possível determinar três temperaturas de pré-transição: 34, 54 e 61ºC; sendo que a temperatura de 54ºC foi evidenciada tanto por fluorescência quanto pela análise sample-sample. Já as temperaturas de 34 e 61ºC foram evidenciadas somente na análise sample-sample. Além disso, a análise variável-variável descreveu a dinâmica conformacional durante o processo de desenovelamento. Assim, pode-se relacionar a temperatura e a dinâmica conformacional. / This work presents a study of the unfolding of papain via temperature. In order to do so, the fluorescence spectroscopy technique was used along with two- dimensional correlation spectroscopy by sample-sample and variable-variable analyses applied to the medium infrared region. Thus, it was possible to determine the three papain thermal pre-transition temperatures, 34, 54 and 61º C. The 54º C one was obtained by fluorescence spectroscopy and sample-sample analyses; whereas the 34 and 61ºC, ones, were detected by sample-sample alone. Additionally, through variable-variable analysis it was possible to describe the conformational dynamics during the unfolding process. Therefore, the relationship between temperature and conformational dynamics could be matched.