Le principal objectif de cette thèse a consisté au développement d’une méthode de screenning pour la découverte de nouvelles réactions de ligations bioorthogonales ainsi que son application sur une bibliothèque développée pour cette étude. Par conséquent, un système de screening a été conçu en trois étapes consistant au départ en une analyse HPLC, puis une évaluation basée sur la fluorescence de haute résolution et finalement un test de microscopie confocal in cellulo. Puis, nous avons standardisé toutes les analyses avec les réactions CuAAC et SpAAC. En outre, nous avons synthétisés 18 réactifs d’intérêts et effectué un screening de 58 expériences de ligation avec une évaluation par méthode HPLC. Parmi les 9 réponses positives obtenues figure 6 réactions impliquant de nouveaux réactifs et les analyses LC‐MS ont pu tous les valider comme des réactions de cycloaddition directe à l’exception d’une réaction. Finalement, nous avons pu appliquer la méthode in cellulo développée, afin d’évaluer la pertinence des réactions de chélation CuAAC pour une application sur cellules. / The main goal of this thesis was the development of a screening method for the discovery of new bioorthogonal ligation reactions as well as its application on a self‐designed library. Therefore we designed a three step screening system consisting of a preliminary HPLC assay, a high resolution fluorescence based assay and a final in cellulo confocal microscopy assay.Subsequently we standardized all assays with the highly established CuAAC and SpAAC. Furthermore, we successfully synthesized 18 reagents of interest and screened 58 ligation experiments with the help of the HPLC setup. The 9 positive hits from this screening contained 6 reactions involving novel reagents and LCMS analysis was able to validate all but one as straight forward cycloaddition reaction. Finally we were able to apply the newly developed in cellulo assay to assess the suitability of chelating CuAAC for in cell application.

In the past two decades, Fluorescence microscopy has imparted tremendous impact in Biology and Imaging. Several super-resolution Fluorescence imaging techniques (e.g. PALM, STED, STORM, 4Pi and structured illumination) have enabled diff raction-unlimited imaging. But high resolution is limited to a depth of few tens of microns. Thus, deep tissue imaging and simultaneous volume imaging have become a highly sought after feature in Fluorescence microscopy. The research work in this thesis address these issues by using spatial filtering techniques to tailor the point spread function (PSF) which uniquely characterizes the optical sys-tem. The advantage of this approach lies in the fact that intricate details about the focal region can be computed and designed with the help of well established theory and experimentation. In particular, this technique was applied to both spherical and cylindrical lenses. The former was used to generate Bessel-like, non-diffracting beams which demonstrated the ability to penetrate deep inside tissue-like media and thereby yielded an imaging depth of nearly 650μm as compared to about 200μm for a state-of-the-art confocal microscope. The latter gave rise to light-sheet and it's extended version that is ideal for planar imaging at large penetration depths. Another development is the generation of multiple light-sheet illumination pattern that can simultaneously illuminate several planes of the specimen. The proposed multiple light-sheet illumination microscopy (MLSIM) technique may enable volume imaging in Fluorescence microscopy. The first two chapters of this thesis are introductory in nature and provides a general overview of the principles of Fluorescence microscopy and three state-of-the-art Fluorescence imaging techniques; namely confocal, multi-photon and light-sheet based microscopy. Confocal microscopes are widely considered as a standard tool for biologists and this discussion shows that even though they have made signi ficant contributions in the fields of biophysics, biophotonics and nanoscale imaging, their inability to achieve better penetration depth has prevented their use in thick, scattering samples such as biological tissue. The system PSF of a confocal microscope broadens as it goes deeper in-side a scattering sample resulting in poor-resolution thereby destroying the very concept of high resolution, noise-free imaging. Additionally, confocal microscopy suffers from in-creased photo-bleaching due to o -layer (above and below the focal plane) excitation and low temporal resolution since it requires point-by-point scanning mechanism. On the other hand, multi-photon microscopy offers several advantages over confocal microscopy such as reduced photo-bleaching and inherent optical sectioning ability, however, it still lacks in providing high temporal resolution. Light-sheet based microscopy have gained popularity in recent years and promises to deliver high spatio-temporal resolution with minimized photo-bleaching. Recently, a considerable amount of research has been dedicated to further develop this promising technique for a variety of applications. The ability to look deeper inside a biological specimen has profound implications. How-ever, at depths of hundreds of microns, several effects (such as scattering, PSF distortion and noise) deteriorates the image quality and prohibits detailed study of key biological phenomenon. Chapter 3 of this thesis describes the original research work which experimentally addresses to this issue. Here, Bessel-like beam is employed in conjugation with an orthogonal detection scheme to achieve imaging at large penetration depth. Bessel beams are penetrative, non-di ffracting and have self-reconstruction properties making them a natural choice for imaging scattering prone specimens which are otherwise inaccessible by other microscopy imaging techniques such as, Widefield, CLSM, 4PI, Structural illumination microscopy and others. In this case such a Bessel-like beam is generated by masking the back-aperture of the excitation objective with a ring-like spatial filter. The proposed excitation scheme allow continuous scanning by simply translating the detection optics. Additionally, only a pencil-like region of the specimen can be illuminated at a given instance thereby reducing premature photobleaching of neighboring regions. This illumination scheme coupled with orthogonal detection shows the ability of selective imaging from a desired plane deep inside the specimen. In such a configuration, the lateral resolution of the illumination arm determines the axial resolution of the overall imaging system. Such an imaging system is a boon for obtaining depth information from any desired specimen layer that includes nano-particle tracking in thick tissue. Experiments performed by imaging the Fluorescent polymer tagged-CaCO3 particles and yeast cell in a tissue-like gel-matrix demonstrates penetration depth that extends up to 650 m. This will advance the field of fluorescence imaging microscopy and imaging. Similar to the ability to observe deep inside a sample, simultaneous 3D monitoring of whole specimens play a vital role in understanding many developmental process in Biology. At present, light-sheet based microscopy is the prime candidate amongst the various microscopy techniques, that is capable of providing high signal-to-background-ratio as far as planar imaging is concerned. Since spatial filtering technique was found to successfully give rise to novel features (such as large penetration depth) in a fluorescence microscope setup, a logical extension would be to implement a similar approach with a light-sheet based microscope setup. These implementations are discussed in Chapter 4 of this thesis where spatial filtering is employed with cylindrical lenses. For facilitating computational and experimental studies, a vectorial formalism was derived to give an explicit computable integral solution of the electric field generated at the focal region of a cylindrical lens. This representation is based on vectorial diffraction theory and further enables the computation of the point spread function of a cylindrical lens. Commonly used assumptions are made in the derivation such as no back-scattering and negligible contribution from evanescent fields. Stationary phase approximation along with the Fresnel transmission coefficients are employed for evaluating the polarization dependent electric field components. Computational studies were carried out to determine the polarization effects and calculate the system resolution. Experimental comparison of light-sheet intensity pro les show good agreement with the theoretical calculations and hence validate the model. This formalism was derived as a first step since it gives the essential understanding of tightly focused E-fields of a high N.A. cylindrical lens systems and thereby helps in further understanding the effect of spatial filtering. As the next step, generation of extended light-sheet for fluorescence microscopy is pro-posed by introducing a specially designed double-window spatial filter at the back-aperture of a cylindrical lens. The filter allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3:38 times for single photon excitation, and 3:68 times for multi-photon excitation as compared to state-of-art single plane illumination microscopy (SPIM) system and essentially implies a larger field of view. Finally, generation of multiple light-sheet pattern is proposed and demonstrated using a different spatial filter placed at the back aperture of a cylindrical lens. A complete imaging setup consisting of multiple light-sheets for illumination and an orthogonal detection arm, is implemented for volume imaging in fluorescence microscopy. This proposed scheme is a single shot technique that enables whole volume imaging by simultaneously exciting multiple specimen layers. Experimental results confirm the generation of multiple light-sheets of thickness 6:6 m with an inter-sheet spacing of 13:4 m. Imaging of 3 5 m sized fluorescently coated Yeast cells (encaged in Agarose gel-matrix) is per-formed and conclusively demonstrates the usefulness and potential of multiple light-sheet illumination microscopy (MLSIM) for volume imaging. As part of the future scope of the research work presented in this thesis, the Bessel-beam based improved depth microscopy technique may attract applications in particle tracking deep inside tissues and optical injection apart from fluorescence imaging applications. The vectorial formalism derived for cylindrical lens can be used to predict other, complex optical setups involving cylindrical lenses. Extended light-sheet generation proposed in this work by using appropriate spatial filtering with a cylindrical lens, complements the existing and popular selective plane illumination microscopy technique and may facilitate the study of large biological specimens (such as, full-grown Zebra sh and tissue) with high spatial resolution and reduced photobleaching. Finally, the MLSIM technique presented in this thesis may accelerate the field of developmental biology, cell biology, fluorescence imaging and 3D optical data storage.

Orientadores: Jose Wilson Magalhães Bassani, Rosana Almada Bassani / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Eletrica e de Computação / Made available in DSpace on 2018-08-09T15:25:46Z (GMT). No. of bitstreams: 1 Soriano_DiogoCoutinho_M.pdf: 3276695 bytes, checksum: c47b4ce326955b65ff10f5c2891b25c2 (MD5) Previous issue date: 2007 / Resumo: No presente trabalho foi desenvolvido um instrumento capaz de quantificar de forma simultânea o encurtamento celular e a concentração citosólica de Ca2+ ([Ca2+]i), utilizando o indicador fluorescente fluo-3. A instrumentação foi aplicada para estudar o papel da ATPase de Ca2+ do RS (SERCA, principal transportador responsável pelo relaxamento celular e pela reposição do estoque de Ca2+ intracelular) na remoção de Ca2+ do citosol em miócitos cardíacos isolados de rato, o que exigiu o desenvolvimento de um protocolo experimental específico. O protocolo experimental desenvolvido consistiu em tornar inoperante o principal competidor da SERCA pelo Ca2+ citosólico, o trocador Na+/Ca2+ (NCX), pela perfusão da célula com solução sem Ca2+ e sem Na+. Nesta situação, considera-se que os demais transportadores de Ca2+ (ATPase de Ca2+ do sarcolema e uniporter mitocondrial de Ca2+) transportem o íon a uma taxa baixa demais para competir com a SERCA. A liberação do Ca2+ do RS foi induzida por pulsos rápidos de cafeína, e foram medidos a amplitude (?[Ca2+]i) e tempo para 50 % de queda (t1/2) dos transientes de [Ca2+]i na ausência e na presença de fármacos que afetam a taxa de captação de Ca2+ pela SERCA. Foram analisados os efeitos do agonista de receptores beta-adrenérgicos isoproterenol (ISO), que promove estimulação da SERCA, e de 2,5-di-(tert-butil) hydroquinona (tBQ), que atua como inibidor da enzima. ISO causou redução significativa do t1/2 de queda do [Ca2+]i (p< 0,01), sem alteração significativa de ?[Ca2+]i (p> 0,05). Já no caso do tBQ, foi observado um aumento significativo do t1/2 de queda do [Ca2+]i (p< 0,01) e redução da ?[Ca2+]i, (p< 0,05). Um modelo teórico da literatura foi adaptado para descrever matematicamente o modelo experimental proposto. As simulações com alterações nos parâmetros cinéticos da SERCA pelos fármacos (de acordo com dados da literatura) foram razoavelmente bem sucedidas em reproduzir os dados experimentais com relação ao tempo de remoção do Ca2+ do citosol. Portanto, foi apresentada aqui uma nova ferramenta experimental e teórica para estudar a captação de Ca2+ pela SERCA em miócitos cardíacos intactos / Abstract: The goal of this work was to develop an instrument for simultaneous measurement of cell shortening and cytosolic Ca2+ concentration ([Ca2+]i), by using the fluorescent Ca2+ indicator fluo-3. The instrument was applied to study the uptake of cytosolic Ca2+ by the sarcoplasmic reticulum (RS) Ca2+- ATPase (SERCA, the main transporter responsible for cell relaxation in intact isolated rat ventricular myocytes). For this purpose, the development of a specific experimental protocol was required. In this protocol, the main competitor of SERCA by cytosolic Ca2+, the Na+/Ca2+ exchanger (NCX), was disabled by removal of extracellular Ca2+ and Na+. In this situation, it may be assumed that the other Ca2+ transporters (sarcolemmal Ca2+-ATPase and mitochondrial Ca2+ uniporter) are too slow to compete with SERCA. SR Ca2+ release was induced by short, rapid caffeine pulses, and the amplitude (?[Ca2+]i) and time for 50% [Ca2+]i decline (t1/2) of the resulting [Ca2+]I transients were measured in the absence and in the presence of drugs that affect the rate of SR Ca2+ uptake by SERCA, namely the beta-adrenergic receptor agonist isoproterenol (ISO), which causes increase in SERCA activity, and 2,5-di-(tert-butyl) hydroquinone (tBQ), which inhibits the enzyme. ISO caused significant reduction of t1/2 (p< 0,01), without any significant change in ?[Ca2+]i (p> 0,05). In case of tBQ, significant increase of t1/2 (p< 0,01) and reduction of ?[Ca2+]I (p< 0,05) were observed. A theoretical model (Tang & Othmer, 1994) was adapted for mathematical description of the experimental model proposed. Simulation of the effects of the drugs, in which SERCA kinetic parameters were changed according to data obtained from literature, were reasonably successful at reproducing the cytosolic [Ca2+]i kinetics observed experimentally / Mestrado / Engenharia Biomedica / Mestre em Engenharia Elétrica

A resposta do sistema nervoso para diversas lesões acarreta a ativação das células gliais entéricas. Este trabalho tem como objetivo analisar o efeito da isquemia e reperfusão intestinal (I/R-i) sobre as células gliais entéricas, neurônios e receptores P2X2 e P2X7. Foram analisados o íleo de ratos Controle, Sham e I/R-i com 0 hora, 24 horas e 14 dias de reperfusão. Foram realizadas dupla marcação dos receptores P2X2 e P2X7 com Hu e S100, densidade, área do perfil e marcação de proliferação celular. Os resultados mostraram dupla marcação de células gliais entéricas e neurônios com os receptores P2X2 e P2X7; a densidade apresentou um aumento de células gliais e diminuição de neurônios imunorreativos ao Hu. A área do perfil de células gliais entericas S100-IR apresentaram diminuição nos grupos I/R-i e foi detectada proliferação de células gliais entéricas nos grupos I/R-i 0 hora e 24 horas. Conclui-se que a isquemia levou a alterações diferenciadas nos receptores P2X2 e P2X7, células gliais entéricas e neurônios, que podem causar disfunções gastrointestinais. / The nervous system response to various injuries involves the activation of enteric glial cells. The aim of the work was to analyze the effect of ischemia and reperfusion (I/R-i) on enteric glial cells, neurons and receptors P2X2 and P2X7. We analyzed the ileum of Control, Sham and I/R-i with 0 hour, 24 hours and 14 days of reperfusion. Double staining were performed P2X2 and P2X7 receptors with Hu and S100, density, area profile and marking of cellular proliferation. The results show double staining of neurons and enteric glial cell with the P2X2 and P2X7; density increased by glial cells and decrease of neurons immunoreactive to Hu. The area profile of enteric glial cell S100-IR showed decreased in Groups I/R-I and enteric glial cell proliferation was observed in groups I/R-i 0 hours and 24 hours. It is concluded that ischemia has led to changes in differential P2X2 and P2X7 receptors, neurons and enteric glial cells, which can cause gastrointestinal dysfunction.

Introdução. O transplante de células é possibilidade terapêutica promissora para muitas doenças neurológicas. Nos últimos anos, a possibilidade do isolamento de células-tronco dos tecidos adultos, por exemplo da medula-óssea, atrai a atenção da comunidade científica, estratégia que minimiza os problemas éticos relativos ao uso de tecido fetal para implantes visando ao tratamento de doenças neurológicas. Entretanto, a eficiência da transdiferenciação de células-tronco mesenquimais em neurônios, bem como os mecanismos envolvidos nesse processo, permanecem desconhecidos. A obtenção de neurônios maduros ocorreu somente em sistemas de co-cultura, o que induz a questão se a diferenciação representa um potencial das células per si, ou se é possível somente devido à fusão com neurônios maduros. Objetivos. No presente trabalho, pretendeu-se verificar o potencial de as células-tronco mesenquimais tornarem-se neurônios e esclarecer os possíveis mecanismos envolvidos nesse processo. Material e métodos. Células-tronco mesenquimais foram isoladas de 20 doadores voluntários normais e caracterizadas por análise de separação celular ativada por fluorescência. A multipotencialidade foi investigada ao se diferenciar as células em condrócitos e osteócitos. A capacidade de auto-renovação foi confirmada pelo ensaio de incorporação de BrdU. Ulteriormente, as células foram diferenciadas por uma semana em meio contendo AMPc, IBMX, ou combinação de ambos, e os resultados foram comparados com o cultivo em meio básico. Diferentes bloqueadores de Ca2+ ou inibidores de PKA foram usados como tentativa de se impedir a diferenciação, ocorrência que foi mensurada com imunocitoquímica para NF-200 (marcador de neurônios maduros). O registro eletrofisiológico por meio de patch clamp foi usado para se confirmar o fenótipo neuronal. As figuras foram configuradas em microscopia confocal. Para análise estatística foi utilizada ANOVA com teste post-hoc. Resultados. As células isoladas expressaram CD90, 105, 44 e 13 mas foram negativas para CD34 e 45. Isto significa que não são de origem hematopoiética; 98,74 ± 0,43% das células incorporaram BrdU em 24 horas. Após o isolamento, foi possível diferenciá-las em condrócitos ou osteócitos. Em situação controle, não foram evidenciadas células positivas para NF200. Por outro lado, ocorreu positividade em 10,75% ± 1,35 (p<0,0001) das células sob IBMX e, em 15,18% ± 1,12, sob a combinação cAMP e IBMX (p<0,0001). Foram registradas correntes de Na+ e K+ dependentes de voltagem, mas não potenciais de ação. A diferenciação foi inibida com PKAi (5,73% ± 0,42, p<0,0001), nifedipina (5,79% ± 0,98, p<0,0001), Ni2+ (7,06% ± 1,68, p<0,0001) e Cd2+ (0 ± 0, p<0,0001). Discussão. Isolou-se uma população de células-tronco estromais da medula-óssea de seres humanos que se mostrou multipotencial e auto-renovável. O aumento da concentração de AMPc no meio elevou a concentração de neurônios para 15%. A diferenciação parece depender da via PKA mas também envolve a concentração intracelular de Ca2+. Conclusão. O correto entendimento de como as células-tronco mesenquimais diferenciam-se pode contribuir para aumentar a eficácia do método e, talvez um dia, tornar possível o uso dessa ferramenta no campo clínico. / Introduction. Cell transplantation has been considered a promising therapeutic approach for many neurological diseases. The possibility of isolation of stem cells from adult tissues, i.e. bone marrow, has attracted the attention of the scientific community in the recent years. This strategy is interesting on avoiding the ethical issues regarding the use of fetal tissue for neural implants. Moreover, the efficiency of the transdifferentiation of mesenchymal stem cells (MSCs) into neurons, and the mechanisms involved in this process remain largely unknown. The obtention of mature neurons was described only in coculture systems, what raised the question if the differentiation is a potential of the cells itself, or if it is possible only due to fusion with mature neurons. Objectives. In the present investigation, we aimed to verify the potential of MSCs to differentiate into neurons, and also to clarify the possible mechanisms involved on it. Material and methods. MSCs were isolated from 20 healthy human subjects and characterized by FACS-analysis. Multipotentiality was addressed by differentiating them into chondrocytes and osteocytes. The self-renewal capacity was confirmed with BrdU-incorporation assay. Afterwards, cells were differentiated for 1 week in a medium containing cAMP, IBMX, or a combination of both, and the results were compared with cells treated in basal-medium condition. Different Ca2+-blockers and PKA-inhibitor peptide were used on an attempt to impair differentiation, which was quantified with NF-200 immunostaining (a marker of mature neurons). Patch-clamp recording was used to confirm neuronal phenotype. Pictures were taken in confocal microscope. For statistical analysis ANOVA with a post-hoc test was used. Results. The isolated cells expressed CD90, 105, 44, and 13, but were negative for CD34 and 45, meaning that they were non-hematopoiethic; 98.74 ± 0.43 % of them incorporated BrdU in 6hs. After isolation, they differentiated into chondrocytes and osteocytes. In a control situation, no NF200 positive cell was seen. On the other hand, 10.75% ± 1.35 (p<.0001) of positivity was seen under IBMX and 15.18% ± 1.12 in the combination of cAMP with IBMX (p<.0001). Na+ and K+-voltage gated currents were recorded. Differentiation was impaired with PKAi (5.73% ± 0.42, p<.0001), nifedipin (5.79% ± 0.98, p<.0001), Ni2+ (7.06% ± 1.68, p<.0001), and Cd2+ (0 ± 0, p<.0001). Discussion. We were able to isolate a population of stromal stem cells from the bone marrow of human subjects, since they were multipotential and self-renewable. Increasing the concentration of cAMP raised the percentage of neurons up to 15%. The differentiation seems to be dependent on the PKA pathway, but also involved the intracellular concentration of Ca2+. Conclusions. The complete understanding of how MSC differentiate can contribute to increase the efficiency of the method and thus make possible to use this powerful tool in the clinical practice.

Chaque cellule humaine est constamment soumise à des agressions extérieures comme l'exposition aux rayons Ultra-Violets, agents chimiques, etc. ou endogènes provenant de la production de métabolites par la cellule elle-même. Ces agressions induisent des dommages dans l'ADN. Ces dommages, s'ils ne sont pas réparés correctement, peuvent induire un dérèglement des fonctions de base de la cellule qui peut alors devenir cancéreuse. Pour réparer leur ADN, les cellules activent divers mécanismes de réparation et établissent une signalisation au niveau des sites endommagés. Dans le noyau, l'ADN est associé à des protéines appelées histones pour former la chromatine. La chromatine se caractérise par différents niveaux d'organisation, aboutissant à la formation d'une structure très compacte. Cette compaction élevée de la chromatine peut représenter une barrière pour la machinerie de réparation. En effet, pour être réparé, l'ADN endommagé doit être accessible à la machinerie de réparation. Pour cela, les cellules ont développé des mécanismes permettant d'accéder à l'ADN endommagé. Ces mécanismes de réponse aux dommages à l'ADN impliquent l'activation de voies de signalisation. L'un des signaux précurseurs activés après dommage à l'ADN est la Poly-ADP-Ribosylation (PARylation). La PARylation est une modification post-traductionnelle composée d'une répétition de petites molécules appelées Poly-ADP-Riboses, qui s'accrochent notamment sur les histones pour signaler la présence de cassures dans l'ADN et permettent ainsi de recruter les protéines impliquées dans la réparation des dommages. Lorsque l'ADN est endommagé, l'activation de processus de réparation induit de manière précoce le recrutement de facteurs de remodelage de la chromatine. Le rôle exact de la signalisation via la PARylation durant les étapes précoces de la réponse aux dommages à l'ADN et plus particulièrement lors du remodelage de la chromatine reste encore mal caractérisé. Durant ma thèse, j'ai utilisé des techniques avancées en microscopie pour étudier la dynamique de la chromatine après induction de dommages à l'ADN. J'ai ainsi tenté d'élucider le rôle de la PARylation dans le mécanisme de remodelage de la chromatine au niveau des dommages dans l'ADN, en recherchant des facteurs permettant d'altérer de manière spécifique la dynamique de la chromatine. Cette méthodologie nous a permis d'identifier différents facteurs impliqués dans le remodelage de la chromatine après dommage à l'ADN. / In each human cell, many thousands of DNA lesions arise every day, challenging continuously the genome integrity. The majority of these lesions results from byproducts of normal cell metabolism or DNA replication, but they are also induced by exposure to radiations and genotoxic chemicals. The integrity of the genome is preserved by a plethora of different DNA damage signalling and repair machinery arranged by the cells. In the cell nucleus, DNA associates with scaffolding proteins to form the chromatin. The chromatin is tightly packed in the nucleus through several levels of organization. Such high-packing state poses a significant challenge for the repair machinery. Indeed, the damaged DNA needs to be accessible to repair proteins, and for that, cells have developed several mechanisms to allow the access to the damaged chromatin. The early steps of the DNA damage response involve the activation of proteins that are part of signalling pathways. One of the proteins activated upon DNA damage is PARP1, which synthetizes long and branched chains of ADP-ribose (poly-ADP-ribose or PAR) on itself and other chromatin factors, including histones. The activation of PARP1 leads to the recruitment of several effectors involved in DNA repair and chromatin remodeling. However the exact function of the PAR-signalling during early DNA damage response and in particular during chromatin remodeling at DNA breaks remains unclear. During my PhD, I used advanced fluorescent imaging tools to study in living cells the dynamics of chromatin in the nucleus at a local scale upon DNA damage. I used these tools to study PAR-dependent chromatin relaxation after DNA damage and to screen factors that selectively alter the dynamic behaviour of the damaged chromatin. This methodology allowed us to identify PAR-dependent factors involved in the local chromatin remodeling upon DNA damage.

Pendant longtemps, la chromatine a été uniquement décrite comme un moyen de compacter près de deux mètres d’ADN dans un noyau de quelques micromètres de diamètre. On sait aujourd’hui que la chromatine représente en fait un élément majeur de régulation de toutes les fonctions nucléaires impliquant l’ADN. Dans le contexte de dommages de l’ADN induits par irradiations UV, la chromatine endommagée subit une décondensation rapide et transitoire qui l’amène à occuper un volume 1,5 fois plus grand que son volume initial. Cette relaxation chromatinienne est associée à une plus grande accessibilité de l’ADN. Néanmoins, le lien entre ces deux effets découlant de la présence de dommages, n’a pas été établi, ni caractérisé. En couplant l’imagerie de cellules vivantes à l’induction de dommages ciblés au sein de noyaux cellulaires par micro-irradiation laser, ces travaux ont permis de mettre en évidence le rôle majeur de PARP1 dans la réponse chromatinienne aux dommages de l’ADN. En effet, certaines conclusions contradictoires présentes dans la littérature scientifique concernant l’action de PARP1 sur la chromatine ont été réconciliées en démontrant que PARP1 seul peut se lier à la chromatine et entraîner une plus forte compaction de celle-ci, tandis que son activité catalytique de PARylation va, quant à elle, conduire à une décompaction de la structure chromatinienne. Cette étude s’est aussi intéressée à la dynamique particulière de l’histone H1 suite aux dommages de l’ADN. En effet, celui-ci est rapidement exclu des zones de dommages par un mécanisme encore inconnu, et les éléments apportés ici suggèrent que H1 pourrait jouer un rôle dans la décondensation de la chromatine suite aux dommages de l’ADN. Pour finir, des techniques de photo-perturbation et de spectroscopie de corrélation de fluorescence ont été employées pour comprendre et caractériser l’environnement moléculaire que constitue la chromatine endommagée et décondensée. Bien qu’une augmentation significative des interactions entre la chromatine et certains de ses partenaires d’interactions soit observée au sein des zones endommagées, aucun changement en termes d’encombrement moléculaire n’a pu être mis en évidence à ce niveau qui pourrait expliquer une plus grande accessibilité de l’ADN. / For a long time, chromatin was only described as a mean to fit the two-meters long DNA molecule into a nucleus of only a few microns. It is admitted today that chromatin actually represents a key element in the regulation of all nuclear functions dependent on DNA. In the context of UV-induced DNA damage, chromatin undergoes a rapid and transient relaxation which leads to an expansion of the damaged area to 1.5 times its original size. While this chromatin response to damage is associated with a higher DNA accessibility, the link between those two phenomena, as well as the mechanisms driving them, are still poorly understood. Using live-cell imaging and laser micro-irradiation to induce DNA damage on specific nuclear areas, this work allowed to gain hindsight on the predominant role played by PARP1 in the DNA damage-induced chromatin relaxation. Indeed, showing that PARP1 at DNA damage sites can both induce chromatin compaction through its recruitment at DNA breaks or chromatin decondensation through its PARylation activity helped reconcile its apparent opposite effects described in the literature. A focus was also made on the linker histone H1, as it displays a peculiar behavior upon DNA damage, being rapidly released from the site of DNA lesions. Even if the driving force behind H1 release from damaged chromatin areas has not been identified yet, its behavior suggests that H1 might play a part in chromatin relaxation or in increasing DNA accessibility upon DNA damage. Lastly, combining photo-activation techniques and fluorescence correlation spectroscopy, experiments were performed in order to understand the physical environment that damaged, relaxed chromatin constitutes. We report here that, while enhanced binding of random DNA binding factors is observed in the damaged chromatin area, no significant change is observed in the macromolecular crowding levels that could potentially explain this enhanced binding, as well as a higher DNA accessibility.

Les complexes acétyltransférases (HAT), SAGA et ATAC, sont des régulateurs de la transcription des gènes. Cependant, peu d’études ont été menées sur la dynamique de ces complexes au niveau cellulaire et sur les mécanismes régulant leur assemblage. Au cours de mes travaux de thèse, j’ai utilisé des approches d’imagerie sur cellules vivantes, afin de déterminer la mobilité de ces complexes en comparaison avec celle d’autres régulateurs transcriptionnels. Les résultats ont montré que les sous-unités de SAGA et ATAC interagissent de manière transiente avec la chromatine. En complément, nous avons montré que les sous-unités spécifiques de SAGA et ATAC (ADA2b et ADA2a) ont des propriétés dynamique intracellulaire différentes et que GCN5, affecte la distribution d’ADA2a. Des analyses protéomique menées sur le comportement de ces protéines au niveau endogène, ont permis de montrer que les voies d’assemblage de ces deux complexes étaient différentes au niveau cytoplasmique et nucléaire. / Human SAGA and ATAC, are histone acetyltransferase (HAT) containing complexes that share a set of subunits and facilitate RNA polymerase II (Pol II) transcription. Little is known for the dynamics of the complexes in living cells and the regulation of their assembly. In this work, we used live-cell imaging to characterise the mobility of the two complexes and compare it with other actors of Pol II transcription. All tested ATAC and SAGA subunits exhibit very transient interactions with chromatin, a property that explains certain aspects of the function of the complexes. Moreover, we showed that overexpressed ATAC- and SAGA-specific HAT-module subunits (ADA2a and ADA2b respectively) have different intracellular dynamics and that the abundance of the shared subunit GCN5, affects the distribution of ADA2a. Quantitative proteomic analysis expanded our findings on endogenous proteins and provided evidence that the cytoplasmic and nuclear assembly pathways of SAGA and ATAC are different.

Abstract Previous reports on the effects of enhanced UV-B radiation on bryophytes have been equivocal. This study shows that mosses not only respond to enhanced UV-B, but they are affected by changes in ambient radiation. The studies were conducted with two model species common in northern environments; red-stemmed feather moss (Pleurozium schreberi) and juniper haircap moss (Polytrichum juniperinum). Both species showed high concentrations of methanol-extractable UV-absorbing compounds (UACs) with high spring-time and early-summer UV, whereas in P. juniperinum, the concentration was affected by early-summer drought. The UACs of P. juniperinum increased again towards autumn suggesting a role in winter hardening. The (spring-time) cell wall-bound UV screen was important to both species. The fundamental adaptation of P. juniperinum to open and exposed environments was reflected in relatively higher concentrations of total UACs compared to P. schreberi. The enhanced UV-B experiments in situ were conducted over two years in Oulu and six years at the FUVIRC site in Sodankylä. Some of the effects of UV-B were seen within the first years of the experiments, or even within hours, while others were observed after several years. Five or six years of enhanced UV-B treatment increased the methanol-extractable UACs of P. schreberi and decreased the green shoot growth of P. juniperinum. The immediate light environment was proposed to have an impact on the varying UAC concentrations. Some mitigating effects of UV-A were observed as well. Off-site measured, reconstructed and modelled UV radiation data was used for comparisons of light environment in situ, or when performing a reconstructive research with historical samples. The environmental sample banks can provide a useful tool to study past environmental conditions, and even reconstruct past radiation levels. It was shown in this study that UACs in P. schreberi and P. juniperinum have fundamental roles as UV-B screens in the cell walls, but there is also a variable response with the soluble fraction that reacts and adapts to the changes in UV radiation. The responses to increasing UV-B radiation vary in magnitude and in time. As P. schreberi and P. juniperinum possess circumboreal and cosmopolitan distributions, the effects of UV-B on these species and consequently on ecosystems has a broad application.

En fournissant l’énergie nécessaire au métabolisme, la phosphorylation oxydative (OXPHOS) est un processus essentiel pour la plupart des organismes vivants. Pour faire face à diverses conditions métaboliques, l’efficacité des chaines respiratoires de la membrane composant l’OXPHOS doit être optimisée. Il est donc important de déterminer les mécanismes qui permettent de réguler l’efficacité de l’OXPHOS en fonction des besoins métaboliques.La question posée est la suivante : existe-t-il une organisation particulière des acteurs de l’OXPHOS dans la membrane des procaryotes qui puisse réguler l’activité de l’OXPHOS ?J’ai étudié l’organisation spatio-temporelle d‘un complexe respiratoire majeur de l’anaérobiose, la nitrate réductase NarGHI chez E. coli. Après avoir créé les outils pour la visualisation de ce complexe dans la cellule, j’ai montré l’existence d’une microcompartimentation de NarGHI aux pôles de la cellule lors d’une respiration en anaérobiose par microscopie optique à fluorescence. Dans un deuxième temps, j’ai montré le caractère dynamique de cette localisation en fonction des conditions métaboliques. L’anaérobiose et la présence d’un ∆pH suffisant sont des éléments requis pour permettre ce niveau d’organisation. Enfin, j’ai démontré que la microcompartimentation de NarGHI aux pôles des cellules augmente le flux d’électrons et l’efficacité des chaines respiratoires associées à la respiration du nitrate.L’ensemble des travaux réalisés au cours de ma thèse permet une meilleure compréhension du processus de l’OXPHOS chez les procaryotes et donne une nouvelle vision des moyens employés pour optimiser l’OXPHOS en fonction des différentes conditions métaboliques. / By providing the energy for the cellular metabolism, oxidative phosphorylation (OXPHOS) is an essential process for most living organisms. In order to thrive, the efficiency of membrane respiratory chains which constitute the OXPHOS must be optimized. Thus it is important to address mechanisms by which the efficiency of the OXPHOS is regulated in response to varying metabolic needs.The question addressed during this PhD is the following: does it exist a specific organization of the OXPHOS components in prokaryotic membranes and does it contribute to the regulation of the OXPHOS process?I have investigated the spatio-temporal organization of a respiratory complex, the nitrate reductase NarGHI of the E. coli bacterium. After creating the tools needed to visualize submicrometrically this complex in the unique cell, I have shown the existence of a polar microcompartimentation during anaerobic respiration using fluorescence microscopy. I have demonstrated the dynamic subcellular organization of NarGHI in response to metabolic conditions. Anaerobiosis and a sufficient ∆pH are cues required to promote such cellular organization. Finally, I have demonstrated that polar microcompartimentation of the complex increases the electron flux and the efficiency of the associated respiratory chains.Overall, these results provide a novel view on OXPHOS in bacterial cells by demonstrating that spatio-temporal organization of a respiratory complex tunes the overall efficiency of the process in response to environmental cues.