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Transcription factors are proteins that regulate transcription of genes by binding to specific DNA sequences proximal to the gene. The specificity and affinity of protein-DNA recognition is critical for proper gene regulation. This thesis explores the mechanisms of binding to the sequence 5’CACGTG, a common recognition sequence both in plants where it is known as the G-box and in mammalian cells where it is termed the E-box. This sequence is of clinical interest because it is the target of the transcription factor Myc, an oncogene linked to many cancers. A number of alpha-helical proteins with different dimerization elements, from the basic region-leucine zipper (bZIP), basic region helix-loop-helix leucine zipper (bHLHZ) and basic region helix-loop-helix-PAS (bHLH-PAS) protein families, are capable of binding to this sequence. The basic regions of all these protein families contain residues that contact DNA and determine DNA sequence specificity while the other subdomains are responsible for dimerization specificity. First, the influence of protein-DNA contacts on sequence specificity of the plant bZIP protein EmBP-1 was probed by point mutations in the basic region. Residues that contact the DNA outside the core G-box sequence and residues that contact the phosphate backbone were found to be important for sequence specificity. Second, the impact of the dimerization subdomains of bHLHZ protein Max, the required heterodimerization partner of the Myc protein, and bHLH-PAS protein Arnt was probed by mutation, deletion and inter-family subdomain swapping studies. All studied protein families are intrinsically disordered, forming structure upon dimerization and DNA binding. The dimerization domains were found to indirectly influence DNA binding by affecting folding, dimerization ability or proper orientation of the basic regions relative to DNA. Lastly, a new strategy for selection of G-box binding proteins in the Yeast One-hybrid system is explored. Together, these studies broaden our understanding of the structure-function relationship of the DNA-binding activities of these closely related families of transcription factors. The creation and characterization of mutants with altered specificity, affinity and dimerization specificity may also be useful for biotechnology applications.

Transcription factors are proteins that regulate transcription of genes by binding to specific DNA sequences proximal to the gene. The specificity and affinity of protein-DNA recognition is critical for proper gene regulation. This thesis explores the mechanisms of binding to the sequence 5’CACGTG, a common recognition sequence both in plants where it is known as the G-box and in mammalian cells where it is termed the E-box. This sequence is of clinical interest because it is the target of the transcription factor Myc, an oncogene linked to many cancers. A number of alpha-helical proteins with different dimerization elements, from the basic region-leucine zipper (bZIP), basic region helix-loop-helix leucine zipper (bHLHZ) and basic region helix-loop-helix-PAS (bHLH-PAS) protein families, are capable of binding to this sequence. The basic regions of all these protein families contain residues that contact DNA and determine DNA sequence specificity while the other subdomains are responsible for dimerization specificity. First, the influence of protein-DNA contacts on sequence specificity of the plant bZIP protein EmBP-1 was probed by point mutations in the basic region. Residues that contact the DNA outside the core G-box sequence and residues that contact the phosphate backbone were found to be important for sequence specificity. Second, the impact of the dimerization subdomains of bHLHZ protein Max, the required heterodimerization partner of the Myc protein, and bHLH-PAS protein Arnt was probed by mutation, deletion and inter-family subdomain swapping studies. All studied protein families are intrinsically disordered, forming structure upon dimerization and DNA binding. The dimerization domains were found to indirectly influence DNA binding by affecting folding, dimerization ability or proper orientation of the basic regions relative to DNA. Lastly, a new strategy for selection of G-box binding proteins in the Yeast One-hybrid system is explored. Together, these studies broaden our understanding of the structure-function relationship of the DNA-binding activities of these closely related families of transcription factors. The creation and characterization of mutants with altered specificity, affinity and dimerization specificity may also be useful for biotechnology applications.

The scope of this work is an in-depth investigation of dielectric mirror microcavities with central organic dye layers, which are preferably modified in at least one lateral dimension. The large quality factor of the planar resonator in conjunction with comparatively stable and spectrally broad emitting molecules allows for a detailed analysis of several aspects of microresonator systems. Their optical properties are analyzed both with transmission and luminescence measurements as well as in the lasing regime. The first part presents the resonant mode properties of planar and laterally structured microcavities. With the help of a high-resolution imaging micro-photoluminescence setup, working either in the spatial (near field) or vectorial (far field) regime, the polarization splitting is studied in a detuned microcavity, containing the dye 4,4'-bis[(N-carbazole)styryl]biphenyl (BSB-Cz) in a matrix of 4,4'-di(N-carbazolyl)- biphenyl (CBP). With the help of a thickness gradient, a relation between the large spectral distance of the cross-polarized states and the mode position within the stop band is investigated. In shadow-mask prepared, laterally restricted devices (5x5 µm2 square boxes), the three-dimensional confinement introduces sets of discrete modes, which experience a similar polarization splitting. The origin in this case is a different phase shift of electromagnetic waves during internal total reflection at a boundary. By using a concentration gradient planar microcavity sample of the dye 4-(dicyanomethylene)-2-methyl-6-(4-(dimethylamino)styryl)-4H-pyran (DCM) in a tris-(8-hydroxyquinoline)aluminum (Alq3) matrix, the influence of the number of emitters on the lasing characteristics is subsequently analyzed. Depending on the pumping conditions, and thus the involvement of the Förster resonant energy transfer, an optimal composition is identified. After a qualitative evaluation of the long-term stability upon various excitation energies, the attention is focussed to the modification of the stimulated emission properties of photonic boxes. The stronger field concentration and altered density of states leads to a significant improvement of the values for the coupling factor fi and the threshold levels. Furthermore, new properties arise, namely simultaneous multimode and off-axis laser emission. With an inhomogeneous excitation of the box, it is possible to selectively excite single modes above the threshold. The work ends with experimental results of metal structures as additional optical element in the organic microcavity layer. Here, the aim is is to understand the passive influence of these possible contact- devices on the lasing performance. For this purpose, the lasing is studied at an interface of an areal thin metal layer, which is incorporated in the organic layer.

Learning to program is acknowledged to be difficult; programming is a complex intellectual activity and cannot be learnt without practice. Research has shown that first year IT students presently struggle with setting up compilers, learning how to use a programming editor and understanding abstract programming concepts. Large introductory class sizes pose a great challenge for instructors in providing timely, individualised feedback and guidance for students when they do their practice. This research investigates the problems and identifies solutions. An interactive and constructive web-based programming environment is designed to help beginning students learn to program in high-level, object-oriented programming languages such as Java and C#. The environment eliminates common starting hurdles for novice programmers and gives them the opportunity to successfully produce working programs at the earliest stage of their study. The environment allows students to undertake programming exercises anytime, anywhere, by "filling in the gaps" of a partial computer program presented in a web page, and enables them to receive guidance in getting their programs to compile and run. Feedback on quality and correctness is provided through a program analysis framework. Students learn by doing, receiving feedback and reflecting - all through the web. A key novel aspect of the environment is its capability in supporting small &quotfill in the gap" programming exercises. This type of exercise places a stronger emphasis on developing students' reading and code comprehension skills than the traditional approach of writing a complete program from scratch. It allows students to concentrate on critical dimensions of the problem to be solved and reduces the complexity of writing programs.

No description available.

[pt] A presente dissertação tem como principal objetivo a conceituação e apresentação das metodologias básicas de previsão de demanda e, a partir de um estudo de caso, a seleção da metodologia mais adequada e sua respectiva implantação. No primeiro capítulo é apresentada, além da importância do referido tema, a empresa selecionada para aplicação dos conceitos levantados, com a descrição de seus principais processos internos. No segundo capítulo foram abordados os conceitos de previsão de demanda e uma revisão dos principais modelos existentes. No capítulo seguinte, o problema que deverá ser tratado com a metodologia proposta é apresentado. Neste momento a metodologia conceituada é aplicada, através da seleção do método de previsão mais adequado ao caso estudado e respectiva modelagem, buscando melhorias em relação aos métodos de previsão existentes na empresa. Neste processo de modelagem utilizou-se o software Forecast Pro, um dos mais conceituados aplicativos de previsão de demanda no mercado. Por fim, na conclusão, avalia-se o impacto das mudanças propostas nos resultados da empresa, principalmente o aumento da precisão da previsão da demanda e, conseqüentemente, redução dos custos de importação e dos índices de stockout. / [en] The main objective of this dissertation is the presentation of basic forecasting methods and their implementation in a case study in supply chain. The first chapter points out the importance of forecasting in this context and describes the company selected for the case study and some of its internal processes that will be under scrutiny in the case study presented in this dissertation. The second chapter discusses the concepts and models of forecasting and reviews some of the major techniques in the field. In chapter three, standard forecasting techniques are apllied to real data (ten time series) from the company and select the most appropriate model in each case. Model adjustment is performed through the Forecast Pro software, one of the best-known products in the market. Chapter four contains the conclusions and the evaluation of the impacts of the proposed methodology on the company s results, especially the increased accuracy of forecasting and, consequently, the reduction in the import costs and stock out index.

[pt] O ONS (operador nacional do sistema elétrico brasileiro) vem utilizando o software ANNSTLF produzido pelo EPRI/EUA (Eletrical Power Research Institute) para realizar a previsão do consumo de carga horária. Entretanto, as estimativas fornecidas pelo programa estão fundamentadas na metodologia de uma rede neural que, de certo modo, impede ao usuário de extrair uma maior interpretação dos resultados que são fornecidos pela rede. Assim sendo, este trabalho pesquisou os métodos univariados convencionais: Holt-Winters e Box e Jenkins, considerando suas formulações aperfeiçoadas e adaptadas às características próprias do tipo de série em questão. Isto é, assumindo a existência de dois ciclos sazonais: um diário e outro semanal. A vantagem destas técnicas univariadas, em comparação ao ANNSTLF, é principalmente a interpretabilidade das informações obtidas. Dessa forma, esta pesquisa permite também avaliar melhor o desempenho do ANNSTLF. / [en] The ONS (National Operator of the Brazilian electrical system) has been using the software ANNSTLF produced by EPRI/USA (Eletrical Power Research Institute) to carry out the forecast of the hourly load consumption. However, the estimates supplied by the program are based on the methodology of a neural net that, in a way, does not allow the user to extract a better interpretation of the results produced by the net. Therefore, investigates the conventional univaried methods: Holt-Winters and Box & Jenkins, considering its formulations perfected and adapted to the characteristics of the series understudy. That is, its assumed the existence of two seasonal cicles: daily and weekly. The advantage of these univariate techniques, in comparison to the ANNSTLF, is mainly the ability to interpret the model estimates. Also, this research also allows a better evaluation the performance of the ANNSTLF.

Submitted by Adriano Duarte da Silva (adriano_duarte_silva@yahoo.com.br) on 2017-03-28T16:30:51Z No. of bitstreams: 1 Dissertacao_Adriano_2016_Completo.pdf: 4047217 bytes, checksum: c2877f83944b388d03457348b61d7d00 (MD5) / Approved for entry into archive by Leiliane Silva (leiliane.silva@fgv.br) on 2017-05-11T13:18:25Z (GMT) No. of bitstreams: 1 Dissertacao_Adriano_2016_Completo.pdf: 4047217 bytes, checksum: c2877f83944b388d03457348b61d7d00 (MD5) / Made available in DSpace on 2017-05-12T12:51:45Z (GMT). No. of bitstreams: 1 Dissertacao_Adriano_2016_Completo.pdf: 4047217 bytes, checksum: c2877f83944b388d03457348b61d7d00 (MD5) Previous issue date: 2016-07-15 / The Brazilian aviation went through moments of supply and demand growth in the last decade, which triggered investment and plan decisions aiming at improving the Brazilian airspace control system and airports infrastructure as well as the services offered by airline companies (for instance aviation fuel demand increase). The main objective of this work is to contribute to the creation of a predictive model of takeoffs and landings for the short and medium run. We use the Box-Jenkins model (ARMA), combined with covariates, to predict the amount of takeoffs and landings of commercial aviation in four Brazilian airports: Galeão Airport (Rio de Janeiro), Brasília Airport (Distrito Federal), Guarulhos Airport (São Paulo) and Recife Airport (Pernambuco). We find that the models fit well in the short run, but in the medium run in forecast events such as the recent Brazilian economic crises can damage the predictions. The data analyzed in this work is owned by The Management Center of Air Navegation (CGNA), which is a military unit subordinated to the Departamento de Controle do Espaço Aéreo (DECEA). Therefore, the predictability of the demand for air traffic will help in the allocation of resources for air traffic management. / A aviação brasileira viveu momentos de crescimentos da oferta e da demanda nos últimos 10 anos, o que gerou a necessidade de planejar e investir no aumento da infraestrutura do Sistema de Controle do Espaço Aéreo Brasileiro (SISCEAB), do parque aeroportuário e dos serviços envolvidos na oferta e na demanda da aviação e das companhias aéreas (exemplo a demanda por Querosene de Aviação – QAV). O principal objetivo deste trabalho é contribuir para a criação de um modelo preditivo do comportamento das operações de pousos e decolagens dos principais aeroportos brasileiros para o curto e médio prazo. Utilizaremos o modelo Box-Jenkins (ARMA), combinado com covariáveis, para prever a quantidade de operações de pousos e decolagens da aviação comercial em quatro aeroportos brasileiros: Aeroporto do Galeão/RJ, Aeroporto de Brasília/DF, Aeroporto de Guarulhos/SP e Aeroporto de Recife/PE. Verificamos que os modelos se ajustam bem no curto prazo, mas que no médio prazo poderão necessitar de mais dados que podem interferir na quantidade de pousos e decolagens de forma atípica, como, por exemplo, a redução da malha aérea devido à crise econômica brasileira dos últimos 2 anos. Os dados utilizados neste trabalho são pertencentes ao Centro de Gerenciamento da Navegação Aérea (CGNA) que é uma unidade militar subordinada ao Departamento de Controle do Espaço Aéreo Brasileiro (DECEA). Portanto, a previsibilidade da demanda de tráfego aéreo ajudará na alocação de recursos no gerenciamento de tráfego aéreo.

Les modifications post-traductionnelles des protéines constituent un niveau crucial de régulation de l’expression des gènes. Parmi elles, la conjugaison peptidique impliquant l’ubiquitine intervient entre autre dans la régulation de la stabilité protéique. La fixation de ce peptide de 76 acides aminés, extrêmement conservé, sous forme de chaîne de polyubiquitine, nécessite l’intervention de trois enzymes (E1, E2 et E3) et constitue un signal de dégradation de la protéine ainsi modifiée. Cette voie de régulation intervient dans de très nombreux processus biologiques. Les complexes SCF sont impliqués dans la voie de protéolyse ciblée. Ils représentent l' une des classes les plus fréquentes d'ubiquitine ligase E3 et ils sont composés de quatre sous-unités (Rbx, Cullin, SKP1, et F-box). La structure et la fonction des complexes SCF, ont été étudiées chez la levure, l’Homme et la plante modèle A. thaliana. Cependant, peu de travaux ont été réalisés chez des plantes cultivées, en particulier les céréales, telles que le blé. Cinq gènes codant pour la sous-unité Skp1 (TSK1, TSK3, TSK6, TSK11 et TSK16), cinq gènes codant pour la sous-unité F-box (ZTL, ATFBL5, EBF, TIR1 et ABA-T), un gène codant pour la sous-unité Cullin1 et un gène codant pour la protéine RBX du complexe SCF du blé, ont été isolés et clonés. Les différents tests d’interaction entre les quatre sous-unités du complexe SCF ont été réalisés par la méthode du double-hybride dans la levure en utilisant la technologie Gateway. Ces études ont montré que les deux protéines, TSK1 et TSK3, fixent spécifiquement différentes sous-unités F-box. Parallèlement, nous avons montré que la protéine TSK11 représente une structure particulière. Des études d’insertion/délétion sur la protéine TSK11 ont permis d’identifier un nouveau domaine indispensable à l’interaction. Les analyses par PCR semi-quantitative des différents gènes codant pour la sous-unité Skp1, dans trois tissus différents (feuille tige et racine), ont mis en évidence une expression constitutive des gènes TSK3, TSK6 et TSK11. Tandis que les gènes TSK1 et TSK16 sont exprimés préférentiellement dans les racines. Les analyses par PCR semi-quantitative sur des plantules de blé à différents stades de développement, ont mis en évidence une surexpression du gène TSK11 au moment de la floraison. Ce qui suggère que TSK11 est probablement un équivalent fonctionnel d’ASK1 chez Arabidopsis thaliana. / The selective degradation of proteins is an important means of regulating gene expression and plays crucial roles in the control of various cellular processes. The Ubiquitin (Ub)–Proteasome System (UPS) is the principal non-lysosomal proteolytic pathway in eukaryotic cells and is required for the degradation of key regulatory proteins. Ubiquitin is a 76-residue protein that can be attached covalently to target proteins through an enzymatic conjugation cascade involving three enzymes denoted, E1, E2 and E3.The SCF complex is a type of ubiquitin-protein ligase (E3) that acts as the specific factor responsible for substrate recognition and ubiquitination. Some polyubiquitinated proteins are then targeted to the 26S proteasome for degradation. The SCF complex consists of four components including SKP1, Cullin1, Rbx1 and a large gene family of F-box proteins. Twenty one SKP1-related genes have been described in the Arabidopsis genome and some of these genes have been analyzed genetically. By contrast, little is known about the function and structure of SKP1 homologues in wheat. Some of the Triticum SKP1-related protein (TSKs) have been characterized in this study. Five complete sequences of SKP1 (TSK1, TSK3, TSK6, TSK11 and TSK16), five F-box (ZTL, ATFBL5, EBF, TIR1 and ABA-T), one Cullin1 and one Rbx, were successfully cloned and biochemically characterized. Yeast two-hybrid analysis showed that TSK1 and TSK3 are capable of interacting with different F-box proteins. Furthermore, TSK11 contains an additional domain that changed its interaction capabilities. In vitro analysis using a chimeric protein showed that this additional domain could modify the interaction between a SKP-like protein and two F-box proteins. Expression analyses revealed that TSK1 and TSK16 were expressed predominantly in roots. While, TSK3, TSK6 and TSK11 were expressed in several wheat organs. In addition, the TSK11 was up-regulated in the leaves at the flowering stage.