Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [114]-128).

Thesis (Ph. D.)--West Virginia University, 2009. / Title from document title page. Document formatted into pages; contains vi, 96 p. : ill. (some col.). Includes abstract. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves [78]-86).

Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (leaves 91-102).

abstract: Why do many animals possess multiple classes of photoreceptors that vary in the wavelengths of light to which they are sensitive? Multiple spectral photoreceptor classes are a requirement for true color vision. However, animals may have unconventional vision, in which multiple spectral channels broaden the range of wavelengths that can be detected, or in which they use only a subset of receptors for specific behaviors. Branchiopod crustaceans are of interest for the study of unconventional color vision because they express multiple visual pigments in their compound eyes, have a simple repertoire of visually guided behavior, inhabit unique and highly variable light environments, and possess secondary neural simplifications. I first tested the behavioral responses of two representative species of branchiopods from separate orders, Streptocephalus mackini Anostracans (fairy shrimp), and Triops longicaudatus Notostracans (tadpole shrimp). I found that they maintain vertical position in the water column over a broad range of intensities and wavelengths, and respond behaviorally even at intensities below those of starlight. Accordingly, light intensities of their habitats at shallow depths tend to be dimmer than terrestrial habitats under starlight. Using models of how their compound eyes and the first neuropil of their optic lobe process visual cues, I infer that both orders of branchiopods use spatial summation from multiple compound eye ommatidia to respond at low intensities. Then, to understand if branchiopods use unconventional vision to guide these behaviors, I took electroretinographic recordings (ERGs) from their compound eyes and used models of spectral absorptance for a multimodel selection approach to make inferences about the number of photoreceptor classes in their eyes. I infer that both species have four spectral classes of photoreceptors that contribute to their ERGs, suggesting unconventional vision guides the described behavior. I extended the same modeling approach to other organisms, finding that the model inferences align with the empirically determined number of photoreceptor classes for this diverse set of organisms. This dissertation expands the conceptual framework of color vision research, indicating unconventional vision is more widespread than previously considered, and explains why some organisms have more spectral classes than would be expected from their behavioral repertoire. / Dissertation/Thesis / Doctoral Dissertation Biology 2016

La mélatonine, hormone "donneuse de temps de l’organisme", en plus de sa synthèse principale dans la glande pinéale est produite dans la rétine où sa régulation et ses fonctions restent partiellement connues chez les mammifères. Le but de mon projet a été de caractériser l’expression temporelle et spatiale de la mélatonine et d’examiner son rôle potentiel dans la physiopathologie rétinienne. Une première partie a révélé au moins deux sites de production de la mélatonine dans la rétine : une synthèse nocturne de l'hormone dans les photorécepteurs de type cône ainsi qu'une production diurne dans les cellules ganglionnaires. Nos résultats ont démontré que la mélatonine peut agir par l'intermédiaire de son récepteur nommé MT1, localisés dans chacune des trois couches rétiniennes. Une seconde partie a mis en évidence que la mélatonine augmente la survie des photorécepteurs chez les rongeurs âgés en modulant l'activation de la voie de survie cellulaire via ses récepteurs MT1 et MT2. / Melatonin, a major hormonal "Zeitgeber" in the body, is produced in the pineal gland as well as the retina. In mammals its regulation and functions in this tissue are only partially understood. The aim of my project was to characterize the temporal and spatial expressions of melatonin as well as its potential roles in retinal physiopathology. In the first part, we identified the timing and sites of melatonin production. Notably, nocturnal synthesis occurs in the cones while diurnal production is seen in the ganglion cells. Our work also establishes that melatonin can act via its MT1-type receptors localized in the three retinal nuclear layers. The second axis demonstrated that melatonin increases photoreceptors viability via its receptors during the course of aging by modulating activation of an intracellular survival pathway.

Understanding how individual photoreceptor cells factor in the spectral sensitivity of a visual system is essential to explain how they contribute to the visual ecology of the animal in question. Existing methods that model the absorption of visual pigments use templates which correspond closely to data from thin cross-sections of photoreceptor cells. However, few modeling approaches use a single framework to incorporate physical parameters of real photoreceptors, which can be fused, and can form vertical tiers. Akaike’s information criterion (AIC c ) was used here to select absorptance models of multiple classes of photoreceptor cells that maximize information, given visual system spectral sensitivity data obtained using extracellular electroretinograms and structural parameters obtained by histological methods. This framework was first used to select among alternative hypotheses of photoreceptor number. It identified spectral classes from a range of dark-adapted visual systems which have between one and four spectral photoreceptor classes. These were the velvet worm, Principapillatus hitoyensis , the branchiopod water flea, Daphnia magna , normal humans, and humans with enhanced S-cone syndrome, a condition in which S-cone frequency is increased due to mutations in a transcription factor that controls photoreceptor expression. Data from the Asian swallowtail, Papilio xuthus , which has at least five main spectral photoreceptor classes in its compound eyes, were included to illustrate potential effects of model over-simplification on multi-model inference. The multi-model framework was then used with parameters of spectral photoreceptor classes and the structural photoreceptor array kept constant. The goal was to map relative opsin expression to visual pigment concentration. It identified relative opsin expression differences for two populations of the bluefin killifish, Lucania goodei . The modeling approach presented here will be useful in selecting the most likely alternative hypotheses of opsin-based spectral photoreceptor classes, using relative opsin expression and extracellular electroretinography.

Les microalgues du phytoplancton sont exposées à des variations fréquentes et rapides de la qualité et de l'intensité spectrale en milieu marin. On peut donc supposer qu'il existe des mécanismes de photoperception spécifiques aux microalgues, différents de ceux identifiés chez les organismes terrestres. L'importance de l'horloge circadienne dans la transmission de l'information lumineuse et notamment la photopériode a largement été caractérisée chez plusieurs organismes modèles terrestres. Le principal objectif de ma thèse était d'étudier les régulations des gènes de l'horloge en réponse à la lumière, chez la microalgue Ostreococcus tauri. Le développement récent des techniques de génomique fonctionnelle chez cette microalgue eucaryote l'a promue comme un nouvel organisme modèle pour l'étude de mécanismes complexes tels que horloge circadienne. Mon étude s'est focalisée sur la caractérisation d'une voie de signalisation de type système à deux composants susceptible de transmettre le signal lumineux vers l'oscillateur central de l'horloge. J'ai étudié les régulations des principaux acteurs de l'horloge d'Ostreococcus par la lumière, et en particulier celles du gène TOC1. J'ai aussi caractérisé la protéine LOV-HK, un nouveau type de photorécepteur à la lumière bleue chez les eucaryotes, dont l'activité est requise pour le bon fonctionnement de l'horloge d'Ostreococcus. L'importance des régulations transcriptionnelles de TOC1 et de LOV-HK, ainsi que leurs fonctions dans l'oscillateur central ont été abordées par l'utilisation d'un promoteur inductible. Enfin, j'ai montré que LOV-HK et plus globalement l'horloge régulent la croissance cellulaire et la biomasse, démontrant leur rôle central dans le contrôle de la physiologie d'Ostreococcus tauri. / Light quality and intensity change frequently in the water column. Therefore marine microalgae are exposed to large changes in light spectrum. Photoperception mechanisms in microalgae are expected to differ from those of land plants since the marine environment has unique properties of light transmission. The focus of my PhD project concerns two mains topics, circadian clock regulation and photoperception in the microalga Ostreococcus tauri. In recent years, O. tauri has emerged as a promising model organism using functional genomics approaches to study complex processes such as the circadian clock regulations. My study was focused on the involvement of a two components system in light transmission to the circadian clock of Ostreococcus. I have studied the molecular mechanisms underlying the regulation of the core clock component TOC1. I have also characterized a novel eukaryotic blue light photoreceptor called LOV-HK, which regulates circadian clock function in Ostreococcus. Using an inducible promoter system to modulate the levels of TOC1 and LOV-HK, I have analyzed the importance of their transcriptional regulations in the clock. Finally, I have shown that LOV-HK and more generally the circadian clock, regulates cell growth and biomass in Ostreococcus tauri.

The first chapter explains the motivation for measuring rod function, in particular the rod’s dynamic recovery from a substantial bleach which results in so-called ‘rate limited’ recovery of sensitivity. The physiological processes that underpin the replenishment of the rod photopigment are described and discussed, and explain the way in which rod function can act as a marker for retinal health. Overall, this chapter explains why rod function is worthy of further investigation.Then follows a description of the experimental methods used in the study of rod function, presented in later chapters. The psychophysical procedures are described and a new method of dark adaptation measurement is presented. The key feature of this technique is a red background.Nonlinear mathematical models are used to describe the reduction in visual thresholds with time following a bleach. Chapter three describes the difficulties associated with numerical methods of nonlinear regression and presents a novel, multi start algorithm that extracts the parameters of interest from a model that adequately describes dark adaptation in the healthy normal subject.Chapter 4 verifies the algorithm presented in chapter 3, which is shown to be reliable and robust. A series of numerical experiments are performed to evaluate some of the characteristics of the algorithm’s performance.In chapter five, a series of experiments are presented to investigate the possible effect of a luminous background on dark adaptation (DA). The first experiment tests whether the rod system can detect a dim red background and the second, whether the rod thresh olds, when measured against light emitted by a red light emitting diode (LED), were linear. The third explores whether the background had any effect on the recovery of rod sensitivity. Finally, conventional contrast sensitivity is used to investigate the recovery from a photo bleach.A novel laboratory based apparatus was used to measure dark adaptation in a group of 36 subjects and the results of these measurements are presented in chapter six. The aim here was to see if the data collected were comparable with the dark adaptation data in the literature. These subjects were asked to make two visits so that an assessment of the test retest reliability of the method could be made. The method is shown to be reliable and capable of characterising the recovery of the visual system after a photo bleach.Although inherently flexible the analogue apparatus was prone to subject driven variability. Greater consistency of measurement was achieved using a digital device developed in partnership with an industry partner, Elektron (UK). This device, described in chapter seven provided fine control of many of the experimental parameters. It was used to measure the dark adaptation of a young healthy group of 21 people.This study uses new methodological approaches, both experimental and statistical, that are robust and reliable to facilitate investigation of rod function, and presents new findings about the early phase of rod sensitivity recovery.

abstract: Patients suffering from Retinitis Pigmentosa (RP), the most common type of inherited retinal degeneration, experience irreversible vision loss due to photoreceptor degeneration. The preservation of cone photoreceptors has been deemed medically relevant as a therapy aimed at preventing blindness in patients with RP. Cones rely on aerobic glycolysis to supply the metabolites necessary for outer segment (OS) renewal and maintenance. The rod-derived cone viability factor (RdCVF), a protein secreted by the rod photoreceptors that preserves the cones, accelerates the flow of glucose into the cone cell stimulating aerobic glycolysis. This dissertation presents and analyzes ordinary differential equation (ODE) models of cellular and molecular level photoreceptor interactions in health and disease to examine mechanisms leading to blindness in patients with RP. First, a mathematical model composed of four ODEs is formulated to investigate the progression of RP, accounting for the new understanding of RdCVF’s role in enhancing cone survival. A mathematical analysis is performed, and stability and bifurcation analyses are used to explore various pathways to blindness. Experimental data are used for parameter estimation and model validation. The numerical results are framed in terms of four stages in the progression of RP. Sensitivity analysis is used to determine mechanisms that have a significant affect on the cones at each stage of RP. Utilizing a non-dimensional form of the RP model, a numerical bifurcation analysis via MATCONT revealed the existence of stable limit cycles at two stages of RP. Next, a novel eleven dimensional ODE model of molecular and cellular level interactions is described. The subsequent analysis is used to uncover mechanisms that affect cone photoreceptor functionality and vitality. Preliminary simulations show the existence of oscillatory behavior which is anticipated when all processes are functioning properly. Additional simulations are carried out to explore the impact of a reduction in the concentration of RdCVF coupled with disruption in the metabolism associated with cone OS shedding, and confirms cone-on-rod reliance. The simulation results are compared with experimental data. Finally, four cases are considered, and a sensitivity analysis is performed to reveal mechanisms that significantly impact the cones in each case. / Dissertation/Thesis / Doctoral Dissertation Applied Mathematics 2020