Plants secrete peptide ligands and use receptor signaling to respond to stress and control development. Understanding the signaling mechanisms and associated molecular trafficking is key to improving plant health and productivity for food, fiber and energy applications. However, one of the challenges to elucidating communication pathways in plants is to study the trafficking of molecules and signals iteratively and non-destructively. This study focuses on using fiber-optic fluorescence microscopy to image live plants iteratively and non-destructively after delivering both labeled and unlabeled phytosulfokine (PSK) into the plant. PSK is a sulfated peptide hormone involved in the regulation of plant cell division and growth via specific receptors, PSKRs. It also plays a role in regulating how plants are able to tolerate stress conditions. The microscope provides two-color (FITC/TRITC) optics and provides high-resolution (3–5 µm) epifluorescence micrographs via a 1-m coherent imaging fiber and a GRIN objective lens. To obtain high-quality images, the fiber was mounted either to a conventional upright microscope body equipped with a leaf compressor, or to a leaf clip with 5-axis positioning (X–Y–Z plus pitch and yaw) mounted on an extensible arm. PSK and TAMRA-labelled PSK were delivered into the roots of various Arabidopsis thaliana genotypes (wt; receptor-deficient: pskr1/pskr2; and tagged receptor overproducing: PSKR1‑GFP), and their movement in roots and leaves was tracked with the fiber-optic fluorescence microscope. Peptide trafficking was successfully observed in live plants non- destructively, confirming that PSK is mobile in both wt and receptor-deficient plants. Preliminary results suggest that the level of receptor PSKR1 may change in response to PSK, and that levels of PSKR1, PSKR2 or both may impact the trafficking of PSK. Understanding how PSK is trafficked in plants will offer insights into how we can improve plants health and productivity.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / During the history of the Civil Engineering, it is witnessed the appearance of a new age, which emphasizes quality in general, and durability, in particular, of the concrete structures. As a result of a continuable search for quality, an evolution in a relatively new field is observed, named Structural Pathology, which relates to the study of structural imperfections in constructions. An efficient solution for this problem is the structural repair, that appears as a strong market share of the industry of the civil construction, motivating the development of a number of materials and procedures of repair that aim to reestablish the original conditions of the damaged structure in order to extend its service life. For the protection and the restoration of the concrete structures, there were developed repair materials destined to different situations of application. The Microscopy, historically applied to the biomedical sciences, field has been spreaded out to the science of the materials field as well, becoming an important tool in the study of diverse properties. The main objective of this research is to investigate the form of linking and bond between repair mortars and concrete, by using microscopy. In this research 247 micrographs were analysed from 24 samples of four types of repair mostars amongst the ones found in the market had been analyzed. The typical morphologic characteristics of those materials were studied through of the optic microscope (OM) and the scanning electron microscope (SEM). The results presented in research provides the understanding of the microscopical analisis related to the bond of someone repair materials. / Ao longo da história da Engenharia Civil, testemunha-se o surgimento de uma nova era, na qual se enfatiza a qualidade em geral e, particularmente, a durabilidade das estruturas de concreto. Como resultado de uma incessante busca pela qualidade, observa-se uma evolução em um campo relativamente novo, designado por Patologia Estrutural, que se relaciona ao estudo de falhas estruturais em obras civis. Uma solução eficaz para este problema é a recuperação estrutural, que surge como um forte segmento de mercado da indústria da construção civil, motivando o desenvolvimento de uma série de materiais e procedimentos de recuperação que visam a restabelecer as condições originais da estrutura danificada e ampliar a sua vida útil. Para a proteção e recuperação das estruturas de concreto, foram desenvolvidos materiais específicos destinados a diferentes situações de aplicação. A microscopia, historicamente aplicada no seguimento das ciências biomédicas, tem sido difundida também para a ciência dos materiais, tornando-se uma ferramenta importante no estudo de diversas propriedades. O objetivo principal deste trabalho é investigar a forma de ligação e aderência entre o concreto e o material de reparo, mediante microscopia. Nesta pesquisa, foram analisadas 247 micrografias em 24 amostras de quatro tipos de argamassas de reparo dentre os encontrados no mercado. As características morfológicas típicas destes materiais foram estudadas com o auxílio do microscópio óptico (MO) e do microscópio eletrônico de varredura (MEV). Os resultados apresentados neste trabalho auxiliam a compreensão da análise microscópica relacionada à aderência de um determinado material de reparo ultilizado. / Mestre em Engenharia Civil

SYRACO est un SYstème de Reconnaissance Automatisée des COccolithes, développé à son origine par Luc Beaufort et Denis Dollfus à partir de 1995 et plus récemment avec Yves Gally. L'utilité d'un tel système est de permettre aux spécialistes un gain de temps majeur dans l'acquisition et le traitement des données. Dans ce travail, le système a été amélioré techniquement et sa reconnaissance a été étendue aux nannofossiles calcaires du Cénozoïque. Ce système fait le tri entre les nannofossiles et les non-nannofossiles avec une efficacité respectivement estimée à 75% et 90 %. Il s'appuie sur une nouvelle base d'images de référence d'espèces datant de l'Eocène Supérieur aux espèces vivantes, ce qui représente des centaines d'espèces avec une forte variabilité morphologique. Il permet de réaliser une classification en 39 morphogroupes par la combinaison de réseaux de neurones artificiels avec des modèles statistiques. Les résultats sont présentés sous forme de comptages automatisés, de données morphométriques (taille, masse...) et de mosaïques d'images. Il peut ainsi être utilisé pour des analyses biostratigraphiques et paléocéanographiques. / SYRACO is an automated recognition system of coccoliths, originally developed since 1995 by Luc Beaufort and Denis Dollfus, and more recently with the help of Yves Gally. The main purpose of this system is for specialists to save time in the acquisition and treatment of data. By this recent work, the system has been technically improved and its ability of recognition has been extended to calcareous nannofossils of the Cenozoic Era. It sorts nannofossils and non-nannofossils with a reliability respectively estimated to 75% and 90%. It is based on a new reference images database of species from the Upper Eocene up to living species. This represents hundreds of species with a high morphological variability. It leads to the establishment of a classification arranged in 39 morphogroups, combining artificial neural networks to statistical models. The results are presented as automated counting, morphometrical data (size, mass...) and mosaics of images. Those results can be valuable in biostratigraphical and paleoceanographical analyses.

The majority of structural studies on DNA have been carried out using fibre diffraction, while studies of its dynamics and thermal behaviour have been mainly performed in solution. When the DNA double helix is heated, it exhibits local separation of the two strands that grow in size with temperature and lead to their complete separation. This work has investigated various aspects of this phenomenon. The experiments reported in this thesis were carried out on films of oriented fibres of DNA prepared with the Wet Spinning Apparatus. Thus, sample preparation and characterisation are essential parts of the research. The structures of two forms of DNA, A and B, have been explored as a function of relative humidity at fixed ionic conditions. A method to eliminate traces of ever-present B-form contamination in A-form samples was established. The high orientation of the DNA molecules within the samples allowed us to investigate dynamical fluctuations and the melting transition of DNA using neutron scattering, which can provide the spatial information crucial to understand a phase transition, probing the static correlation length along the molecule as a function of temperature. The transition has been investigated for A and B-forms in order to understand its dependence on molecular configuration.Furthermore, after the first melting, denatured DNA films show typical glass behaviour. Their thermal relaxation has been explored using calorimetry.Neutron and X-ray inelastic scattering (INS and IXS) were used in the past to measure longitudinal phonons in fibre DNA, and the results shown disagreement. Recent INS measurements supported with phonon simulations have been crucial to understand the different dispersion curves reported to date. Experiments using INS and IXS have been carried out to continue with this investigation. Attempts to observe the transverse fluctuations associated to the thermal denaturing of DNA, never experimentally investigated before, have been made.

La majorité des études structurales sur l’ADN avaient été réalisées par diffraction sur des fibres tandis que ses propriétés dynamiques thermiques avaient été étudiées en solution. Lorsque la double hélice d’ADN est chauffée elle présente des séparations locales des deux brins, dont la taille augmente avec la température jusqu’à la séparation complète des brins. Ce travail étudie différents aspects de ce phénomène. Les expériences présentées dans cette thèse ont été réalisées sur des films formés de fibres orientées d’ADN préparés par la méthode du ”filage humide“. La préparation et la caractérisation des échantillons en deux formes A et B de l’ADN ont constitué une partie importante de la recherche. Une méthode pour éliminer la contamination résiduelle de la forme B dans les échantillons de forme A a été mise au point. La bonne orientation des molécules d’ADN dans les échantillons nous a permis d’étudier les fluctuations dynamiques et la transition de dénaturation thermique de l’ADN par diffraction de neutrons, sensibles à la longueur de corrélation statique le long de la molécule en fonction de la température. La transition a été étudiée pour les formes A et B pour déterminer comment elle dépend de la conformation. De plus, après la première dénaturation thermique, les films d’ADN présentent un comportement typique d’un verre. Leur relaxation thermique a été étudiée par calorimétrie. La diffusion inélastique de neutrons et de rayons X (INS et IXS) avaient été utilisées antérieurement pour mesurer les phonons longitudinaux dans des fibres d’ADN, avec des désaccords entre les résultats. Des mesures INS récentes, complétées par des simulations, avaient été cruciales pour comprendre les différentes courbes de dispersion observées. Nous avons mené des expériences INS et IXS pour poursuivre cette analyse. Des tentatives pour observer les mouvements transversaux associés à la dénaturation thermique de l’ADN, jamais observés expérimentalement, ont également été faites. / The majority of structural studies on DNA have been carried out using fibre diffraction, while studies of its dynamics and thermal behaviour have been mainly performed in solution. When the DNA double helix is heated, it exhibits local separation of the two strands that grow in size with temperature and lead to their complete separation. This work has investigated various aspects of this phenomenon. The experiments reported in this thesis were carried out on films of oriented fibres of DNA prepared with the Wet Spinning Apparatus. Thus, sample preparation and characterisation are essential parts of the research. The structures of two forms of DNA, A and B, have been explored as a function of relative humidity at fixed ionic conditions. A method to eliminate traces of ever-present B-form contamination in A-form samples was established. The high orientation of the DNA molecules within the samples allowed us to investigate dynamical fluctuations and the melting transition of DNA using neutron scattering, which can provide the spatial information crucial to understand a phase transition, probing the static correlation length along the molecule as a function of temperature. The transition has been investigated for A and B-forms in order to understand its dependence on molecular configuration.Furthermore, after the first melting, denatured DNA films show typical glass behaviour. Their thermal relaxation has been explored using calorimetry.Neutron and X-ray inelastic scattering (INS and IXS) were used in the past to measure longitudinal phonons in fibre DNA, and the results shown disagreement. Recent INS measurements supported with phonon simulations have been crucial to understand the different dispersion curves reported to date. Experiments using INS and IXS have been carried out to continue with this investigation. Attempts to observe the transverse fluctuations associated to the thermal denaturing of DNA, never experimentally investigated before, have been made.