Thesis (M.S.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 68 pages. Includes Vita. Includes bibliographical references.

Les processus de plasticité cérébrale entrainés par la perte visuelle restent un domaine méconnu dans le champ des neurosciences. La vision centrale et périphérique, le meilleur compromis évolutionniste entre une bonne résolution spatiale et un volume d’espace échantillonné maximal, sont traitées par des régions différentes du cerveau. Par conséquent, étudier et comprendre l’impact de la perte visuelle centrale ou périphérique dans ces régions constitue une étape cruciale dans l’étude du cerveau visuel. Afin d’étudier ces processus, nous avons utilisé deux modèles de perte visuelle sélective de la vision centrale (la dystrophie maculaire de Stargardt) et périphérique (la rétinopathie pigmentaire), et nous avons évalué l’impact à terme de ces deux types de désafférentation sur la structure et la connectivité fonctionnelle du cerveau. 1. Plasticité structurelle induite par la perte sélective de la vision centrale ou périphérique. Nous avons étudié l’épaisseur corticale (EpCo) et de l’entropie corticale (EnCo, marquer de complexité synaptique) du lobe occipital, région pour laquelle nous disposons d’une cartographie complète des régions cytoarchitectoniques. Nous avons constaté que la perte de la vision centrale induit un amincissement des régions appartenant au flux dorsal, tandis que la perte de la vision périphérique occasionne un amincissement du cortex visuel primaire (CVP), ainsi que des régions du flux ventral et dorsal. Ces effets étaient inattendus si on se rapporte au modèle canonique qui associe la vision centrale au flux ventral et la vision périphérique au flux dorsal. La normalité de l’EnCo dans ces régions, suggère que la complexité synaptique est préservée dans les réseaux neuronaux résiduels. Nous avons identifié des modifications de l’EnCo seulement en cas de perte de la vison centrale, où l’augmentation de l’EnCo dans des régions impliquées dans la reconnaissance des objets pourrait traduire une réponse adaptative à la perte de la haute résolution spatiale de cette partie du champ visuel. Cette augmentation de la complexité synaptique pourrait compenser une éventuelle perte neuronale et être responsable de la normalité de l’EpCo dans ces régions. 2. Plasticité de la connectivité fonctionnelle des régions du cortex visuel primaire recevant les projections de la partie centrale » et périphérique champ visuel Dans cette étude, nous avons exploré et comparé la connectivité fonctionnelle des régions afférentées et desafférentées du CVP de sujets souffrant de dystrophie maculaire de Stargardt et retinitis pigmentosa, avec les régions afféréntées correspondantes du CVP de sujets avec une vision normale. Cette étude a révélé une réorganisation fonctionnelle distincte du CVP afférenté et désafférenté. Ainsi, le CVP qui reçoit les afférences visuelles résiduelles présente une connectivité fonctionnelle accrue avec des régions voisines, probablement afin de favoriser le traitement de l’information visuelle, tandis que le CVP désafférenté augmente sa connectivité fonctionnelle avec des régions plus éloignées, vraisemblablement pour contribuer aux fonctions supérieures et à des processus de type top-down. L’analyse comparative des données morphologiques et fonctionnelles suggère une correspondance des régions amincies du cortex visuel associatif avec des régions qui montrent une diminution de la connectivité fonctionnelle avec le CVP périphérique, et des régions présentant une augmentation de la complexité synaptique avec des régions qui montrent une connectivité fonctionnelle accrue avec le CVP périphérique. Ces données suggèrent que la désafferentation sensorielle du CVP périphérique est plus propice au développement d’une réorganisation cérébrale. Synoptique : Ces travaux révèlent un aspect inattendu de la plasticité cérébrale induite une perte isolée de la vision centrale ou périphérique. La réorganisation s’avère plus complexe que le laisser présager le modèle canonique actuel, vraisemblablement trop simple. / Cerebral plasticity induced by visual loss represents a poorly understood field of neuroscience, with numerous questions that don’t yet have an answer. Central and peripheral vision, the evolutionary compromise between spatial resolution and the sampled space volume, are processed in distinct areas of the brain. Understanding the impact of vision loss in theses regions, is of utmost interest for the study of visual brain. Herein, in two models of retinal disorders affecting central and peripheral vision (namely Stargardt macular dystrophy and retinitis pigmentosa), we specifically investigated the effects of the central and peripheral visual loss on brain morphology and its functional connectivity. 1. Morphological plastic changes induced by central and peripheral visual loss. We explored the effects of visual loss on cortical thickness (CoTks) and cortical entropy (CoEn, marker of synaptic complexity) in the cytoarchytectonic regions of the occipital lobe. Central visual loss associated thinning in dorsal stream regions, while peripheral visual loss in early visual cortex (EVC) and regions belonging both to dorsal and ventral stream. Theses effects were unpredicted by the canonical view “central vision – ventral stream”, “peripheral vision – dorsal stream”. Normal CoEn in theses areas suggests that synaptic complexity is preserved in the remaining networks. Only central visual field loss presented CoEn alterations, namely an increase in areas involved in object recognition, that likely reflects a synaptic complexity enhancement in response to the loss of the high spatial resolution of central vision. The gain in synaptic complexity could mask neuronal loss due to deafferentation and may account for the CoTks normality. 2. Plastic changes in the functional connectivity of central and peripheral EVC. We explored and compared to normally afferented EVC, the functional connectivity of afferented and deafferented parts of EVC and found that central and peripheral visual loss induce different patterns of reorganization. Residually afferented early visual cortex reinforce local connections presumably to enhance the processing of altered visual input, while deafferented EVC strengthen long-range connections presumably to assist high-order functions. Combined structural and functional data indicate that areas with reduced CoTks superpose with several areas presenting reduced functional connectivity with the peripheral EVC and that areas with increased CoEn superpose with several areas presenting increased functional connectivity with afferented peripheral EVC. These data point that alterations of the sensory input to the peripheral field are more prone to induce plastic changes. Overview : Data in the current work provide an interesting perspective about the plasticity following central or peripheral visual field loss and show that it is more complex than the canonical model would have let to presume.

The body of work presented here is a compendium of the multiple steps required for an investigator initiated trial of an existing medication (Valproic Acid- VPA) for a new indication (Retinitis Pigmentosa – RP). The chapters are listed in logical and chronological order of the process. In order to access patient records an expedited Institutional Review Board (IRB) application for retrospective chart review was submitted (Chapter 1). These records enabled the statistical analysis which not only laid the framework for the trial design, but also became the basis for two manuscripts (Chapter 2). Protocol development informed by the preliminary human studies (Chapter 3) was an instrumental part of the Investigational New Drug (IND) application (Chapter 3.5). This protocol along with the extensive case report forms that detail the intended data to be collected are included in the IND application. Because the Phase II clinical trial proposed attempting to identify the specific RP mutations of the subjects utilizing a National Eye Institute (NEI) study that enabled free genotyping services, two IRB applications were submitted (Chapter 3.6). The first was for approval of the NEI genotyping protocol, the second involved the VPA intervention. Two very different sources of funding for this trial were attempted (Chapter 4) – the NIH via the Challenge Grant mechanism and a private eye disease foundation (Foundation Fighting Blindness). In Chapter 5 I detail the alternate study designs that were considered and developed for this trial (and ultimately abandoned). Finally, in Chapter 6, I formally detail my suggestions to aid in the development of a comprehensive investigator initiated core facility at UMMMC. The goal of this project was two-fold. The first was to learn the entire process of trial and protocol design both from a Umass Institutional perspective as well as from the perspective of the FDA. The second goal was the very real prospect of helping patients with a blinding disease. This work was successful on both counts. IRB approval was received for all the submitted applications. The complexity and uniqueness of many aspects of these submissions culminated in a comprehensive learning experience. The process of working with the Umass Research Pharmacy as well as developing the industry contacts and know-how to develop a workable and financially feasible placebo were both particularly important learning experiences. FDA approval of the IND submission was also received, and the process of pre-communication and delving into the considerable and ever-changing rules and regulations resulted in an extensive and valuable knowledge base. While the practicality of funding has limited the ability of this trial to move forward at this point, given the extensive framework laid by this body of work, we are actively pursuing other opportunities. The third outcome of this work, while not as intentional, was the considerable process of determining the specific competencies and infrastructure that exist at UMMMC to enable investigator initiated drug intervention studies. While this institution is clearly moving rapidly in the direction of translational research, the many needs of these studies are often only clearly understood when the process is specifically undertaken. In completing the approval of this Phase II clinical trial, I was not only able to better understand and define the existing capabilities of UMMMC for this kind of research, I was able to add to that infrastructure when the existing knowledge or skill set was not available. In this manner, I was able to inform and guide many of the support personnel who guided me and have become a part of the strategic direction of UMMMC towards clinical translational research.

Avancement dans l'acquisition d'image et le progrès dans les méthodes de traitement d'image ont apporté les mathématiciens et les informaticiens dans les domaines qui sont d'une importance énorme pour les médecins et les biologistes. Le diagnostic précoce de maladies (comme la cécité, le cancer et les problèmes digestifs) ont été des domaines d'intérêt en médecine. Développement des équipements comme microscope bi-photonique à balayage laser et microscope de fluorescence par réflexion totale interne fournit déjà une bonne idée des caractéristiques très intéressantes sur l'objet observé. Cependant, certaines images ne sont pas appropriés pour extraire suffisamment d'informations sur de cette image. Les méthodes de traitement d'image ont été fournit un bon soutien à extraire des informations utiles sur les objets d'intérêt dans ces images biologiques. Rapide méthodes de calcul permettent l'analyse complète, dans un temps très court, d'une série d'images, offrant une assez bonne idée sur les caractéristiques souhaitées. La thèse porte sur l'application de ces méthodes dans trois séries d'images destinées à trois différents types de diagnostic ou d'inférence. Tout d'abord, Images de RP-muté rétine ont été traités pour la détection des cônes, où il n'y avait pas de bâtonnets présents. Le logiciel a été capable de détecter et de compter le nombre de cônes dans chaque image. Deuxièmement, un processus de gastrulation chez la drosophile a été étudié pour observer toute la mitose et les résultats étaient cohérents avec les recherches récentes. Enfin, une autre série d'images ont été traités où la source était une vidéo à partir d'un microscopie photonique à balayage laser. Dans cette vidéo, des objets d'intérêt sont des cellules biologiques. L'idée était de suivre les cellules si elles subissent une mitose. La position de la cellule, la dispersion spatiale et parfois le contour de la membrane cellulaire sont globalement les facteurs limitant la précision dans cette vidéo. Des méthodes appropriées d'amélioration de l'image et de segmentation ont été choisies pour développer une méthode de calcul pour observer cette mitose. L'intervention humaine peut être requise pour éliminer toute inférence fausse. / Advancement in Image Acquisition Equipment and progress in Image Processing Methods have brought the mathematicians and computer scientists into areas which are of huge importance for physicians and biologists. Early diagnosis of diseases like blindness, cancer and digestive problems have been areas of interest in medicine. Development of Laser Photon Microscopy and other advanced equipment already provides a good idea of very interesting characteristics of the object being viewed. Still certain images are not suitable to extract sufficient information out of that image. Image Processing methods have been providing good support to provide useful information about the objects of interest in these biological images. Fast computational methods allow complete analysis, in a very short time, of a series of images, providing a reasonably good idea about the desired characteristics. The thesis covers application of these methods in 3 series of images intended for 3 different types of diagnosis or inference. Firstly, Images of RP-mutated retina were treated for detection of rods, where there were no cones present. The software was able to detect and count the number of cones in each frame. Secondly, a gastrulation process in drosophila was studied to observe any mitosis and results were consistent with recent research. Finally, another series of images were treated where biological cells were observed to undergo mitosis. The source was a video from a photon laser microscope. In this video, objects of interest were biological cells. The idea was to track the cells if they undergo mitosis. Cell position, spacing and sometimes contour of the cell membrane are broadly the factors limiting the accuracy in this video. Appropriate method of image enhancement and segmentation were chosen to develop a computational method to observe this mitosis. Cases where human intervention may be required have been proposed to eliminate any false inference.

Le syndrome de Bardet-Biedl (BBS) est considéré comme l’une des causes les plus fréquentes de rétinopathie pigmentaire dite syndromique. Il a été démontré une connexion entre les protéines BBS et les structures du cil primaire. Le cil primaire est un organelle formé par une fine évagination de la membrane plasmique soutenu par une ossature de microtubules. Dans la rétine, le photorécepteur (PR) est une cellule ciliaire composée d’un segment interne et d’un segment externe reliés par un cil primaire modifié. Au cours de ce travail, nous avons mis en évidence que le stress du réticulum endoplasmique est à l’origine du processus apoptotique car un défaut ciliaire dans le PR entraine l’accumulation de protéines dans le segment interne et déclenche une réponse au stress cellulaire appelé unfolded protein response. Nous avons développé un traitement pharmacologique modulant ce stress cellulaire afin de ralentir l’apoptose des PR dans un modèle murin BBS. Cette approche pharmacologique a montré son efficacité dans le maintien et la fonctionnalité des PR. Elle pourrait potentiellement être applicable à d’autres ciliopathies rétiniennes. / Bardet-Biedl syndrome (BBS) is one of the most frequent cause of syndromic retinitis pigmentosa. BBS proteins are related to primary cilium structure and function. The primary cilium is microtubule-based antenna-like structure at the surface of the cell. In the retina, the photoreceptor (PR) is a ciliated cell composed of an inner and an outer segment linked by a modified primary cilium. In this study, we demonstrated that endoplasmic reticulum stress induces unfolded protein response due to protein accumulation in the inner segment in case of ciliary defect in the PR leading to apoptosis. We designed a pharmacological treatment to alleviate PR apoptosis in a BBS mouse model. This pharmacological approach was efficient to protect PR from apoptosis and maintain their functionality. This treatment could be applicable to others retinal ciliopathies.

Retinitis Pigmentosa (RP) is an incurable inherited retinal degeneration affecting approximately 1 in 4,000 individuals globally. The aim of this dissertation was to identify drugs that can help patients suffering from the disease. To accomplish this goal, the zebrafish was utilized as a model for RP to perform <i>in vivo</i> drug screening. The zebrafish RP model expresses a human rhodopsin transgene which contains a premature stop codon at position 344 (<i>Tg</i>(<i>rho:Hsa.RH1_Q344X</i>)). This zebrafish model exhibits significant rod photoreceptor degeneration beginning at 7 days post fertilization (dpf). To assess the visual consequence of this rod degeneration the zebrafish behavior visual motor response (VMR) was assayed under scotopic conditions. The Q344X RP model larvae displayed a deficit in this VMR in response to a scotopic light offset. This deficit in behavior was utilized to perform a drug screen to identify compounds that could ameliorate the deficient Q344X VMR. The ENZO SCREEN-WELL® REDOX library was chosen to be screened since oxidative stress may increase RP progression in a non-specific manner. From this library, a β-blocker, carvedilol, was identified as a compound that improved the Q344X VMR behavior. This drug was also able to increase rod number in the Q344X retina. Carvedilol was shown to be capable of working directly on rods by demonstrating that the drug can signal through the adrenergic pathway in the rod-like human Y79 cell line. Since carvedilol is an FDA-approved drug, this screening paradigm was utilized to screen the Selleckchem FDA-approved library to identify more drugs that can potentially be repurposed to treat RP like carvedilol. Additionally, this scotopic VMR assay was used to demonstrate that it can identify behavioral deficits in the P23H RP model zebrafish<i> (Tg</i>(<i>rho:Hsa.RH1_P23H</i>)). This dissertation work provides a potential FDA-approved drug for RP treatment and sets the foundation for future drug screening to identify more drugs to treat different forms of RP.

Retinitis Pigmentosa (RP) is an inherited photoreceptor degenerative disease that leads to blindness and affects about 1 in 4000 people worldwide. The disease is predominantly caused by mutations in genes expressed exclusively in the night active rod photoreceptors; however, blindness results from the secondary loss of the day active cone photoreceptors, the mechanism of which remains elusive. Here, we show that the mammalian target of rapamycin complex 1 (mTORC1) is required to delay the progression of cone death during disease and that constitutive activation of mTORC1 is sufficient to maintain cone function and promote cone survival in RP. Activation of mTORC1 increased expression of genes that promote glucose uptake, retention and utilization, leading to increased NADPH levels; a key metabolite for cones. This protective effect was conserved in two mouse models of RP, indicating that the secondary loss of cones can be delayed by an approach that is independent of the primary mutation in rods. However, since mTORC1 is a negative regulator of autophagy, its constitutive activation led to an unwarranted secondary effect of shortage of amino acids due to incomplete digestion of autophagic cargo, which reduces the efficiency of cone survival over time. Moderate activation of mTORC1, which promotes expression of glycolytic genes, as well as maintains autophagy, provided more sustained cone survival. Together, our work addresses a long-standing question of non-autonomous cone death in RP and presents a novel, mutation-independent approach to extend vision in a disease that remains incurable.

<p>For many years, researchers have developed ways to diagnose degenerative disease in the retina by utilizing multiple gene analysis techniques. Retinitis pigmentosa (RP) disease can cause either partially or totally blindness in adults. For that reason, it is crucial to find a way to pinpoint the causes in order to develop a proper medication or treatment. One of the common methods is genome-wide analysis (GWA). However, it cannot fully identify the genes that are indirectly related to the changes in eye size. In this research, RNA sequencing (RNA-seq) analysis is used to link the phenotype to genotype, creating a pool of candidate genes that might associate with the RP. This will support future research in finding a therapy or treatment to cure such disease in human adults.</p> <p><br></p> <p>Using the Drosophila Genetic Reference Panel (DGRP) – a gene reference panel of fruit fly – two types of datasets are involved in this analysis: eye-size data and gene expression data with two replicates for each strain. This allows us to create a phenotype-genotype map. In other words, we are trying to trace the genes (genotype) that exhibit the RP disease guided by comparing their eye size (phenotype). The basic idea of the algorithm is to discover the best replicate combination that maximizes the correlation between gene expression and eye-size. Since there are 2N possible replicate combinations, where N is the number of selected strains, the original implementation of sequential algorithm was computationally intensive.</p> <p><br></p> <p>The original idea of finding the best replicate combination was proposed by Nguyen et al. (2022). In this research, however, we restructured the algorithms to distribute the tasks of finding the best replicate combination and run them in parallel. The implementation was done using the R programming language, utilizing doParallel and foreach packages, and able to execute on a multicore machine. The program was tested on both a laptop and a server, and the experimental results showed an outstanding improvement in terms of the execution time. For instance, while using 32 processes, the results reported up to 95% reduction in execution time when compared with the sequential version of the code. Furthermore, with the increment of computational capabilities, we were able to explore and analyze more extreme eye-size lines using three eye-size datasets representing different phenotype models. This further improved the accuracy of the results where the top candidate genes from all cases showed connection to RP.</p>

No description available.

No description available.