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Open Access Publications from the University of California

Scholarly Works (41 results)

  • Thesis
  • Peer Reviewed
UC Santa Barbara Electronic Theses and Dissertations (2022)

The development of the central nervous system (CNS), which includes the brain, requires the coordination of numerous intricate processes. Due to its complexity, the brain can be a difficult tissue to use to investigate the genes that are involved in regulating these processes. The retina, which is a simpler tissue in the CNS, can be utilized to study the mechanisms that underlie proper development and maintenance. The murine retina, in which numerous cell types have been studied, provides researchers with a model to study. In this dissertation, three genes and their involvement in retinal development will be evaluated. In the first chapter, we utilize 26 recombinant inbred (RI) strains in order to elucidate genes, as well as their genetic variants, that regulate the size of a neuronal cell population, the AII amacrine cell. In the second chapter, we investigate the genetic regulation of neuronal migration during retinal development. The final chapter describes the analysis of a cell-type specific transcription factor that regulates the morphology of that cell. Studying the genes that regulate the development of the retina provides insight to how the nervous system develops, the knowledge of which should ultimately contribute to the design of successful therapeutics, particularly those involving cell and gene replacement strategies.

    Cover page: Genetic Regulation of Retinal Development
    • Article
    • Peer Reviewed
    UC Santa Barbara Previously Published Works (2012)
      Cover page: Retinal Mosaics: Pattern Formation Driven by Local Interactions between Homotypic Neighbors
      • Article
      • Peer Reviewed
      UC Santa Barbara Previously Published Works (2018)
        Cover page: Axon Terminal Arbors of Retinal Horizontal Cells Lose Control
        • Thesis
        • Peer Reviewed
        UC Santa Barbara Electronic Theses and Dissertations (2017)

        The central nervous system, is composed of several complex tissues that serve a wide variety of critical functions. One of these tissues residing in the eye, the retina, serves to convert incoming photons of light to neural signals that aid in the perception of vision. The retina is comprised of various cellular populations that each develop through unique set of mechanisms, many of which remained to be elucidated. In this dissertation, we have examined the genetic mechanisms underlying how specific populations of cells in the retina develop, in order to more fully understand how individual populations arise and therefore gain insight into how these populations may interact with one another in the mature retina. First, we sought to uncover genes that modulate neuronal cell number. Through the use of a forward genetic screen, we were able to study the development of the mouse retina across genetically dissimilar strains and identify genes that modulate retinal development. We uncovered a role for two novel genes, Xkr8 and Ggct, in the modulation of bipolar cell number and pursued an investigation into the genetic variants underlying cell number differences across inbred mouse strains. Secondly, we sought to elucidate novel mechanisms by how the glial population of astrocytes develop. We identified an unknown function for the gene Sox2 in the development of astrocytes as well as the retinal vasculature. Taken together, these analyses provide insight into how both neuronal and glial cell populations develop in the mouse retina. Both of these cellular populations are critical to a functioning retina and by understanding the specific mechanisms underlying how they develop, we begin to uncover how the complexity of the central nervous system arises.

          Cover page: Genetic Determinants of Retinal Cell Development
          • Article
          • Peer Reviewed
          UC Santa Barbara Previously Published Works (2018)
          The present study has taken advantage of publicly available cell type specific mRNA expression databases in order to identify potential genes participating in the development of retinal AII amacrine cells. We profile two such genes, Delta/Notch-like EGF repeat containing (Dner) and nuclear factor I/A (Nfia), that are each heavily expressed in AII amacrine cells in the mature mouse retina, and which conjointly identify this retinal cell population in its entirety when using antibodies to DNER and NFIA. DNER is present on the plasma membrane, while NFIA is confined to the nucleus, consistent with known functions of each of these two proteins. DNER also identifies some other subsets of retinal ganglion and amacrine cell types, along with horizontal cells, while NFIA identifies a subset of bipolar cells as well as Muller glia and astrocytes. During early postnatal development, NFIA labels astrocytes on the day of birth, AII amacrine cells at postnatal (P) day 5, and Muller glia by P10, when horizontal cells also transiently exhibit NFIA immunofluorescence. DNER, by contrast, is present in ganglion and amacrine cells on P1, also labeling the horizontal cells by P10. Developing AII amacrine cells exhibit accumulating DNER labeling at the dendritic stalk, labeling that becomes progressively conspicuous by P10, as it is in maturity. This developmental time course is consistent with a prospective role for each gene in the differentiation of AII amacrine cells.
            Cover page: DNER and NFIA are expressed by developing and mature AII amacrine cells in the mouse retina
            • Article
            • Peer Reviewed
            UC Santa Barbara Previously Published Works (2018)
            The orderly spacing of retinal neurons is commonly regarded as a characteristic feature of retinal nerve cell populations. Exemplars of this property include the horizontal cells and the cholinergic amacrine cells, where individual cells minimize the proximity to like-type neighbors, yielding regularity in the patterning of their somata. Recently, two types of retinal bipolar cells in the mouse retina were shown to exhibit an order in their somal patterning no different from density-matched simulations constrained by soma size but being otherwise randomly distributed. The present study has now extended this finding to a type of retinal amacrine cell, the AII amacrine cell. Voronoi domain analysis revealed the patterning in the population of AII amacrine somata to be no different from density-matched and soma-size-constrained random simulations, while analysis of the density recovery profile showed AII amacrine cells to exhibit a minimal intercellular spacing identical to that for those random simulations: AII amacrine somata were positioned side-by-side as often as chance would predict. Regularity indexes and packing factors (PF) were far lower than those achieved by either the horizontal cells or cholinergic amacrine cells, with PFs also being comparable to those derived from the constrained random simulations. These results extend recent findings that call into question the widespread assumption that all types of retinal neurons are assembled as regular somal arrays, and have implications for the way in which AII amacrine cells must distribute their processes to ensure a uniform coverage of the retinal surface.
              Cover page: The somal patterning of the AII amacrine cell mosaic in the mouse retina is indistinguishable from random simulations matched for density and constrained by soma size
              • Article
              • Peer Reviewed
              UC Santa Barbara Previously Published Works (2015)
              Most structures within the central nervous system (CNS) are composed of different types of neuron that vary in both number and morphology, but relatively little is known about the interplay between these two features, i.e. about the population dynamics of a given cell type. How such arrays of neurons are distributed within a structure, and how they differentiate their dendrites relative to each other, are issues that have recently drawn attention in the invertebrate nervous system, where the genetic and molecular underpinnings of these organizing principles are being revealed in exquisite detail. The retina is one of the few locations where these principles have been extensively studied in the vertebrate CNS, indeed, where the design principles of 'mosaic regularity' and 'uniformity of coverage' were first explicitly defined, quantified, and related to each other. Recent studies have revealed a number of genes that influence the formation of these histotypical features in the retina, including homologues of those invertebrate genes, although close inspection reveals that they do not always mediate comparable developmental processes nor elucidate fundamental design principles. The present review considers just how pervasive these features of 'mosaic regularity' and 'uniform dendritic coverage' are within the mammalian retina, discussing the means by which such features can be assessed in the mature and developing nervous system and examining the limitations associated with those assessments. We then address the extent to which these two design principles co-exist within different populations of neurons, and how they are achieved during development. Finally, we consider the neural phenotypes obtained in mutant nervous systems, to address whether a prospective gene of interest underlies those very design principles.
                Cover page: Design principles and developmental mechanisms underlying retinal mosaics
                • Article
                • Peer Reviewed
                UC Santa Barbara Previously Published Works (2016)
                The mature retinal architecture is composed of various types of neuron, each population differing in size and constrained to particular layers, wherein the cells achieve a characteristic patterning in their local organization. These demographic features of retinal nerve cell populations are each complex traits controlled by multiple genes affecting different processes during development, and their genetic determinants can be dissected by correlating variation in these traits with their genomic architecture across recombinant-inbred mouse strains. Using such a resource, we consider how the variation in the numbers of twelve different types of retinal neuron are independent of one another, including those sharing transcriptional regulation as well as those that are synaptically-connected, each mapping to distinct genomic loci. Using the populations of two retinal interneurons, the horizontal cells and the cholinergic amacrine cells, we present in further detail examples where the variation in neuronal number, as well as the variation in mosaic patterning or in laminar positioning, each maps to discrete genomic loci where allelic variants modulating these features must be present. At those loci, we identify candidate genes which, when rendered non-functional, alter those very demographic properties, and in turn, we identify candidate coding or regulatory variants that alter protein structure or gene expression, respectively, being prospective contributors to the variation in phenotype. This forward-genetic approach provides an alternative means for dissecting the molecular genetic control of neuronal population dynamics, with each genomic locus serving as a causal anchor from which we may ultimately understand the developmental principles responsible for the control of those traits.
                  Cover page: Genomic control of neuronal demographics in the retina
                  • Thesis
                  • Peer Reviewed
                  UC Santa Barbara Electronic Theses and Dissertations (2014)

                  The present study examined the role of alternative splicing as a mechanism to create neuronal diversity within the developing retina. The Isl1 gene has two alternatively spliced isoforms, α and β, that are present in the developing retina. The Isl1β isoform lacks a critical portion of a protein-binding domain with which Isl1 binds to Lhx3 in a known transcriptional complex (Isl1:Lhx3:Ldb1). Developmental analysis of Isl1 expression reveals the Isl1α isoform is expressed at higher levels than Isl1β throughout development and persisting into adulthood. Isl1 isoforms are present in distinct subsets of retinal ganglion cells, with Isl1β-expressing cells being restricted to cells with soma sizes under 175μ2. A luciferase assay demonstrates the Isl1β isoform is functionally distinct from Isl1α and is not capable of activating the Isl1:Lhx3:Ldb1 complex as Isl1α is. These results suggest that Isl1β containing-complexes may have unique gene targets from Isl1α and implicate the alternative splicing of Isl1 as a mechanism contributing to neuronal differentiation during retinal development.

                    Cover page: Transcriptional Activation by Islet1 Isoforms
                    • Article
                    • Peer Reviewed
                    UC Santa Barbara Previously Published Works (2014)
                    Retinal neurons are often arranged as non-random distributions called "mosaics," as their somata minimize proximity to neighboring cells of the same type. The horizontal cells serve as an example of such a mosaic, but little is known about the developmental mechanisms that underlie their patterning. To identify genes involved in this process, we have used three different spatial statistics to assess the patterning of the horizontal cell mosaic across a panel of genetically distinct recombinant inbred strains. To avoid the confounding effect of cell density, which varies twofold across these different strains, we computed the "real/random regularity ratio," expressing the regularity of a mosaic relative to a randomly distributed simulation of similarly sized cells. To test whether this latter statistic better reflects the variation in biological processes that contribute to horizontal cell spacing, we subsequently compared the genomic linkage for each of these two traits, the regularity index, and the real/random regularity ratio, each computed from the distribution of nearest neighbor (NN) distances and from the Voronoi domain (VD) areas. Finally, we compared each of these analyses with another index of patterning, the packing factor. Variation in the regularity indexes, as well as their real/random regularity ratios, and the packing factor, mapped quantitative trait loci to the distal ends of Chromosomes 1 and 14. For the NN and VD analyses, we found that the degree of linkage was greater when using the real/random regularity ratio rather than the respective regularity index. Using informatic resources, we narrowed the list of prospective genes positioned at these two intervals to a small collection of six genes that warrant further investigation to determine their potential role in shaping the patterning of the horizontal cell mosaic.
                      Cover page: The patterning of retinal horizontal cells: normalizing the regularity index enhances the detection of genomic linkage
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