AcrA is the periplasmic component of an efflux system AcrA-AcrB-TolC, which can expel different classes of antibiotics. AcrB is the inner membrane (IM) pump that utilizes proton-motive force for the active transport, TolC is the outer membrane (OM) channel, and AcrA coordinates the actions of AcrB and TolC, so that substrates are expelled across the two membranes, bypassing the periplasm. It has been proposed that AcrA either provides a static seamless link between AcrB and TolC, or acts like its analogous viral membrane fusion protein (MFP) and actively brings the IM and OM closer for substrate transfer. To better understand the role of AcrA in the efflux mechanism, site-directed spin labeling (SDSL)/EPR (electron paramagnetic resonance) spectroscopy is used to investigate the structure and dynamics of AcrA in solution. My results demonstrated that AcrA is a dynamic protein that undergoes pH-dependent and reversible conformational changes. AcrA contains an interrupted alpha-helical, coiled-coil domain flanked by a pair of beta-stranded lipoyl motifs, and my SDSL/EPR analysis revealed that the pH-induced conformation change mainly involves the coiled-coil and the lipoyl domains. In addition, I found that each AcrA monomer folds into an intra-molecular hairpin and AcrA monomers oligomerize with their coiled-coil hairpins aligned in parallel. Unlike the pH-induced conformational rearrangement of a viral MFP, change in pH alters both intra- and inter-molecular interaction along the coiled-coil of AcrA without rearranging the hairpin fold. The organization of AcrA protomers and its pH-induced conformational switching are, however, congruent with the TolC coiled-coil hairpins in the iris-like opening of the TolC channel. Together, my studies suggest that rather than being a passive structural linkage between AcrB and TolC, AcrA plays an active role mediating the drug efflux. The reported AcrA dynamics provides new insights into the AcrA-TolC interactions for the channel opening during the efflux process.

MRI can provide anatomical, functional, and physiological images at relatively high spatial resolution and is non-invasive and does not have depth limitation. However, the application of MRI to study the retina is difficult due to the very small size of the retina. This thesis details the development of MRI methods to image blood flow (BF), anatomy, and function of the retina and choroid, and their application to two diseases of the retina: diabetic retinopathy and retinal degeneration. A unique continuous arterial spin labeling technique was developed to image BF in mice and tested by imaging cerebral BF. This method was then applied to image layer-specific BF of the retina and choroid in mice, and to acquire BF functional MRI of the retina and choroid in response to hypoxic challenge. Additionally blood oxygen level dependent functional MRI of the mouse retina and choroid in response to hypoxic challenge was obtained using a balanced steady state free precession sequence which provides fast acquisition, has high signal to noise ratio, and does not have geometric distortion or signal dropout artifacts. In a mouse model of diabetic retinopathy, MRI detected reduced retinal BF in diabetic animals. Visual function in the diabetic mice, as determined by psychophysical tests, was also reduced. Finally, in a mouse model of retinal degeneration, BF and anatomical MRI detected reductions of retinal BF and the thickness of the retina. The studies detailed in this thesis demonstrate the feasibility of layer-specific MRI to study BF, anatomy, and function, in the mouse retina. Further, these methods were shown to provide a novel means of studying animal models of retinal disease in vivo.

Microvascular lesions of the brain are observed in numerous pathological conditions including Alzheimer's disease (AD). Regional patterns of microvascular abnormality can be characterized using current neuroimaging technologies. When applied to mouse models of human disease, these technologies reveal cerebral vascular patterns and help uncover genotype-to-phenotype relationships. This thesis focuses on the development and testing of techniques for measuring two perfusion-related metrics in mouse brain regions, namely, cerebral blood volume (CBV) and cerebral blood flow (CBF) using micro-computed tomography (micro-CT) and arterial spin labeling (ASL), respectively. The main developments for measurement of CBV have included: refinements to micro-CT specimen preparation; registration of micro-CT images to an MRI anatomical brain atlas; and masking of major vessels to calculate small-vessel CBV (sv-CBV). The development of this micro-CT technique provided reference values of CBV over neuroanatomical brain regions in wildtype mice. A separate study was conducted to assess regional sv-CBV in a mouse model of AD; this study was motivated by the prevalence of microvascular lesions in patients who suffer from AD. Significant regional differences in sv-CBV were found between AD-afflicted mice and controls. The main developments for measurement of CBF have included: design and implementation of accurate ASL slice positioning and optimization of inversion efficiency parameters. The development of this ASL technique provided reference values of CBF over neuroanatomical brain regions in wildtype mice. These techniques for measuring CBV and CBF over mouse brain regions could lead to improved characterization of vascularity in models of neurological diseases.

Microvascular lesions of the brain are observed in numerous pathological conditions including Alzheimer's disease (AD). Regional patterns of microvascular abnormality can be characterized using current neuroimaging technologies. When applied to mouse models of human disease, these technologies reveal cerebral vascular patterns and help uncover genotype-to-phenotype relationships. This thesis focuses on the development and testing of techniques for measuring two perfusion-related metrics in mouse brain regions, namely, cerebral blood volume (CBV) and cerebral blood flow (CBF) using micro-computed tomography (micro-CT) and arterial spin labeling (ASL), respectively. The main developments for measurement of CBV have included: refinements to micro-CT specimen preparation; registration of micro-CT images to an MRI anatomical brain atlas; and masking of major vessels to calculate small-vessel CBV (sv-CBV). The development of this micro-CT technique provided reference values of CBV over neuroanatomical brain regions in wildtype mice. A separate study was conducted to assess regional sv-CBV in a mouse model of AD; this study was motivated by the prevalence of microvascular lesions in patients who suffer from AD. Significant regional differences in sv-CBV were found between AD-afflicted mice and controls. The main developments for measurement of CBF have included: design and implementation of accurate ASL slice positioning and optimization of inversion efficiency parameters. The development of this ASL technique provided reference values of CBF over neuroanatomical brain regions in wildtype mice. These techniques for measuring CBV and CBF over mouse brain regions could lead to improved characterization of vascularity in models of neurological diseases.

Cette thèse porte sur le développement de nouvelles approches par marquage de spin suivi par spectroscopie RPE. Cette technique est bien adaptée pour suivre la dynamique structurale des protéines. Son principe repose sur l'insertion d'un radical nitroxyde, en un (ou plusieurs) site(s) choisi(s) d'une protéine et permet de sonder localement la structure de la protéine étudiée grâce aux différentes techniques de RPE (en onde continue et impulsionnelle).Dans une première partie, cette technique a été appliquée à la caractérisation de la dynamique structurale de l'IF1 de levure, un peptide inhibiteur de l'ATP-synthase. L'utilisation des spectroscopies de RPE et de dichroïsme circulaire a permis de montrer qu'IF1 de levure dimérise par sa partie médiane et que la partie C-terminale est désordonnée.La seconde partie est plus méthodologique et a pour but d'étudier et de caractériser un marqueur nouvellement synthétisé afin d'élargir les potentialités du marquage de spin. En effet, cette technique est notamment limitée par la faible diversité spectrale offerte par les sondes disponibles (trois raies). Le nouveau marqueur donne un spectre RPE à six raies grâce à la présence d'un noyau magnétique dans l'environnement du radical. Greffé sur une protéine modèle, nous avons montré que ce nouveau marqueur est tout autant capable de rendre compte de variations structurales qu'un marqueur classique. La superposition des signatures spectrales (trois raies + six raies) montre qu'il est possible de différencier les deux signatures spectrales et de sonder simultanément deux sites d'une protéine et de son partenaire. / This thesis focuses on the development of new approaches for site-directed spin labeling followed by EPR spectroscopy. This technique is well suited to monitor the structural dynamics of proteins. The insertion of a nitroxide radical, in one (or several) selected site(s) of a protein, allows probing the structure of the protein using different EPR spectroscopy approaches (continuous wave and pulsed).In a first part, this technique has been applied to characterize the structural dynamics of the yeast IF1, an inhibitory peptide of the ATP-synthase. Using EPR and circular dichroïsm spectroscopies we showed that yeast IF1 dimerizes by its central part and that the C-terminal part remains disordered.The second part is more methodological and the aim is to study and characterize a newly synthesized spin label in order to expand the potential of site-directed spin labeling. In particular, the technique is limited by the poor spectral diversity offered by the available labels (three lines). The new label gives a six lines EPR spectrum thanks to the presence of a magnetic nucleus in the environment of the radical. Grafted on a model protein, we demonstrated that this new label is as able as classical ones to report on structural variations. The superposition of the spectral signatures (three lines + six lines) showed that it is possible to differentiate the two spectral signatures and to probe two sites of a protein and its partner simultaneously.

The cytoskeletal protein vinculin plays a key role in the control of cell-cell or cell-matrix adhesions. It is involved in the assembly and disassembly of focal adhesions and affects their mechanical stability. While many facts highlight the importance and significance of vinculin for vital processes, its precise role in the regulation of cell adhesions is still only partially understood. Various EPR methods are used in this work in order to study the vinculin tail (Vt) domain in an aqueous buffer solution and its structural changes induced by F-actin and acidic phospholipids. EPR results in combination with a rotamer library approach (RLA), MD simulation and other computational methods allowed the construction of molecular models of Vt and dimeric Vt in the presence and absence of its binding partners. Furthermore, X-band orientation selective DEER measurements were applied on a Vt double mutant. It could be shown that the determination of the mutual orientation of protein bound spin labels is possible at X-band frequencies, if the orientation correlation of the spin label pair is strong. The method established here can be used to determine valuable information about proteins and nucleic acids, expanding the virtue of DEER spectroscopy as a tool for structure determination.

Arterial spin labeling (ASL) perfusion Magnetic Resonance Imaging (MRI) is a noninvasive technique for measuring quantitative cerebral blood flow (CBF) but subject to an inherently low signal-to-noise-ratio (SNR), resulting in a big challenge for data processing. Traditional post-processing methods have been proposed to reduce artifacts, suppress non-local noise, and remove outliers. However, these methods are based on either implicit or explicit models of the data, which may not be accurate and may change across subjects. Deep learning (DL) is an emerging machine learning technique that can learn a transform function from acquired data without using any explicit hypothesis about that function. Such flexibility may be particularly beneficial for ASL denoising. In this dissertation, three different machine learning-based methods are proposed to improve the image quality of ASL MRI: 1) a learning-from-noise method, which does not require noise-free references for DL training, was proposed for DL-based ASL denoising and BOLD-to-ASL prediction; 2) a novel deep learning neural network that combines dilated convolution and wide activation residual blocks was proposed to improve the image quality of ASL CBF while reducing ASL acquisition time; 3) a prior-guided and slice-wise adaptive outlier cleaning algorithm was developed for ASL MRI. In the first part of this dissertation, a learning-from-noise method is proposed for DL-based method for ASL denoising. The proposed learning-from-noise method shows that DL-based ASL denoising models can be trained using only noisy image pairs, without any deliberate post-processing for obtaining the quasi-noise-free reference during the training process. This learning-from-noise method can also be applied to DL-based ASL perfusion prediction from BOLD fMRI as ASL references are extremely noisy in this BOLD-to-ASL prediction. Experimental results demonstrate that this learning-from-noise method can reliably denoise ASL MRI and predict ASL perfusion from BOLD fMRI, result in improved signal-to-noise-ration (SNR) of ASL MRI. Moreover, by using this method, more training data can be generated, as it requires fewer samples to generate quasi-noise-free references, which is particularly useful when ASL CBF data are limited. In the second part of this dissertation, we propose a novel deep learning neural network, i.e., Dilated Wide Activation Network (DWAN), that is optimized for ASL denoising. Our method presents two novelties: first, we incorporated the wide activation residual blocks with a dilated convolution neural network to achieve improved denoising performance in term of several quantitative and qualitative measurements; second, we evaluated our proposed model given different inputs and references to show that our denoising model can be generalized to input with different levels of SNR and yields images with better quality than other methods. In the final part of this dissertation, a prior-guided and slice-wise adaptive outlier cleaning (PAOCSL) method is proposed to improve the original Adaptive Outlier Cleaning (AOC) method. Prior information guided reference CBF maps are used to avoid bias from extreme outliers in the early iterations of outlier cleaning, ensuring correct identification of the true outliers. Slice-wise outlier rejection is adapted to reserve slices with CBF values in the reasonable range even they are within the outlier volumes. Experimental results show that the proposed outlier cleaning method improves both CBF quantification quality and CBF measurement stability. / Electrical and Computer Engineering

La perfusion est un facteur important dans la viabilité et la fonction du myocarde. Des atteintes microvasculaires diffuses, précédant l'infarctus ou l'insuffisance cardiaque sont impliqués dans bon nombre de pathologies cardiaques. Ce travail vise à améliorer les techniques existantes de mesure quantitatives et non-invasive de la perfusion myocardique par marquage de spins artériels (ASL). La première partie de mon travail de thèse a consisté en la mise place chez la souris d'une technique alternative pour mesurer la perfusion myocardique. Celle-ci est basée sur un marquage pulsé et régulièrement répété afin de construire un état d'équilibre de l'aimantation sous l'influence de la perfusion (approche steady-pulsed ASL). Le modèle théorique associé à cette technique spASL a été développé en parallèle afin de quantifier le flux sanguin tissulaire. Il a été montré que spASL permettait d'obtenir un résultat similaire aux techniques existantes avec en plus, les avantages d'améliorer la sensibilité au signal de perfusion ainsi que de réduire le temps d'acquisition. Dans un second temps, un transfert vers l'imagerie clinique pour une application chez l'homme a été entrepris. Le marquage de type spASL a été conservé et le module de lecture a été adapté aux spécificités de l'imagerie cardiaque chez l'homme pour une acquisition en respiration libre. Un post-traitement dédié qui comprend une correction de mouvement rétrospective a ensuite vu le jour afin d'améliorer la robustesse de nos mesures. Parallèlement aux développements conduits chez l'homme, nous avons exploité l'approche spASL chez l'animal en proposant diverses améliorations en fonction des études menées. / Myocardial blood flow is an important factor of tissue viability and function. Diffuse changes in microcirculation preceding heart failure are involved in various cardiac pathologies. This work aim at improving existing techniques allowing quantitative and non-invasive myocardial perfusion assessment using arterial spin labeling. The first step of my work was to design an alternative approach to quantify myocardial blood flow in mice. The so called steady-pulsed ASL (spASL) is based on a regularly repeated pulsed labeling in order to build up a stationary regime of the magnetization under the influence of perfusion. The associated theoretical model has been developed in parallel to quantify tissue blood flow. We have shown that spASL allows to obtain similar results than the previously employed techniques, with the additional advantages of an increased sensitivity to the perfusion signal and a reduced acquisition time. A transfer towards clinical imaging for human applications was then undertaken. The spASL labeling scheme has been preserved while adapting the readout module to the specificities of cardiac MRI when applied to free-breathing human acquisitions. A dedicated post-processing, which includes a retrospective motion correction, has emerged subsequently to improve the robustness of our measurements. In parallel to the developments made for human studies, some optimization of the spASL technique when applied to rodent have been carried out depending on the conducted studies.

A esquizofrenia é um transtorno psiquiátrico incapacitante que afeta estimadamente 1% da população mundial. Delírios, alucinações, desorganização de pensamento e prejuízo cognitivo são as principais marcas da Esquizofrenia. Fisiologicamente, além de anormalidades funcionais e estruturais, alterações na atividade neuronal são reportadas. Como a atividade neuronal possui uma relação direta com o fluxo sanguíneo cerebral (CBF, Cerebral Blood Flow), a técnica de Imagens por Ressonância Magnética, denominada Marcação dos Spins Arteriais (ASL, Arterial Spin Labeling), que permite a obtenção de mapa quantitativo de CBF, é uma ferramenta útil na avaliação funcional cerebral. Além disso, a ASL pode ser usada na avaliação da conectividade funcional, que é eficiente na investigação de rupturas funcionais entre as regiões do cérebro. Comparando com um grupo de sujeitos saudáveis, os pacientes com esquizofrenia, recrutados no Hospital das Clínicas de Ribeirão Preto (HCFMRP), apresentaram redução de CBF em regiões bilaterais do polo frontal e giro frontal superior, giro frontal medial direito, partes triangular e opercular do giro frontal inferior direito, divisão posterior do giro supramarginal esquerdo, divisão superior e inferior do córtex occipital lateral esquerdo e polo occipital. A conectividade funcional, avaliada por três diferentes métodos (baseado em semente, análise de componentes independentes e teoria dos grafos), se apresentou prejudicada em regiões envolvendo funções motoras, sensoriais e cognitivas dos pacientes. Portanto, utilizando uma técnica de imagem completamente não invasiva, foi possível observar déficits de CBF e alterações na organização funcional do cérebro de pacientes com esquizofrenia, relacionados com os sintomas e características da psicopatologia. / Schizophrenia is a disabling psychiatric disorder that affects around 1% of the population worldwide. Delusions, hallucinations, disorganized thought, and cognitive deficits are the main features of schizophrenia. Physiologically, in addition to functional and structural abnormalities, changes in neuronal activity are reported. Since the Cerebral Blood Flow (CBF) is directly related with neuronal activity, the Magnetic Resonance Imaging (MRI) technique called Arterial Spin Labeling (ASL), which allows the quantification of CBF, is a useful tool in brain functional evaluation. In addition, ASL can be used to assess functional connectivity, which is efficient in investigating functional impairment between regions of the brain. Patients with Schizophrenia, recruited at the Clinical Hospital (HCFMRP), presented a reduction of CBF in bilateral regions of the frontal pole and superior frontal gyrus, right medial frontal gyrus, triangular and opercular parts of the right inferior frontal gyrus, posterior division of left supramarginal gyrus, superior and inferior division of left lateral occipital cortex and occipital pole. Functional connectivity, assessed by three different methods (seed-based, independent component analysis and graph theory), was impaired in regions involving patients\' motor, sensory and cognitive functions. Therefore, using a noninvasive imaging technique, it was possible to observe CBF deficits and alterations in the functional organization of the brain of schizophrenia patients, related to the symptoms and characteristics of the psychopathology.

O processo de envelhecimento é acompanhado por um declínio nas funções cognitivas, principalmente, de funções fluidas ou de processamento. Essas diminuições são pelo menos, em parte, devido a alterações estruturais e funcionais do sistema nervoso central. Uma abordagem para estudar as mudanças funcionais é a medição da utilização metabólica regional da glicose, ou, alternativamente, um parâmetro físico correlacionado ao metabolismo cerebral e à atividade funcional local, como o fluxo sanguíneo cerebral (CBF). Neste contexto, em Imagens por Ressonância Magnética (IRM), a técnica de Marcação dos Spins Arteriais (ASL) surge como uma importante ferramenta não invasiva para análises perfusionais. Seu uso não só permite avaliar a perfusão sanguínea cerebral, gerando mapas quantitativos de CBF, mas também fornecer uma alternativa para estudar a conectividade funcional (FC), um parâmetro importante para descrição da topologia e funcionalidade cerebral. Sessenta e três indivíduos saudáveis, na faixa etária entre dezoito à setenta e dois anos, foram recrutados para participar deste estudo. Análises estatísticas mostram uma diminuição de CBF em várias regiões cerebrais, especialmente nos lobos frontal e temporal, que acompanham o processo de envelhecimento. As medidas de FC foram obtidas em análises por regiões de interesse e teoria de grafos; estas também demostraram uma diminuição, com o avanço da idade, em regiões presentes nos lobos frontal e temporal, mas também relataram um maior número de regiões prejudicadas no lobo parietal. Portanto, usando uma técnica de imagem não invasiva, foi possível observar déficits de CBF além de alterações de aspectos da organização funcional, oferecendo valores quantitativos que podem ajudar na melhor descrição dos efeitos do envelhecimento na hemodinâmica cerebral. / Aging process is accompanied by a decline in cognitive functions foremost comprise fluid or processing-based functions. These decreases are at least partly due to structural and functional deteriorating changes of the central nervous system. One approach to study these functional changes is the measurement of the regional metabolic utilization of glucose, or, alternatively, a physical quantity correlated to cerebral metabolism and local functional activity, such as the cerebral blood flow (CBF). In this context, Arterial spin labeling (ASL) emerges as a noninvasive Magnetic Resonance Imaging (MRI) perfusion technique. Its use not only allows assessing cerebral perfusion, by generating CBF values, but also can provide an alternative to study functional connectivity (FC), which is an important parameter that describes the brain topology and functionality. Sixty-three healthy subjects, from age eighteen to seventy-two years, were recruited to participate in this study. ASL-CBF maps showed a decrease in several brain regions, especially in frontal and temporal lobes that follows aging process. FC measures were assessed with regions of interest (ROI-to-ROI) and graph theory analysis, also showing a decrease in regions present in frontal and temporal lobes, and also more impaired regions in the parietal lobe. Therefore, using a noninvasive imaging technique it was possible to observe CBF deficits besides alteration in aspects on functional organization, offering quantitative values that can help to describe better the aging effects on cerebral hemodynamics.