The development of the diencephalon can be summarised as a process in which cells that initially appear similar give rise to a complex structure that contains a variety of cell groups called nuclei. It involves two stages: the early patterning of the diencephalic prosomeres and the later formation of the individual nuclei. It has been shown that transcription factors and morphogens regulate the first stage but their further effects on the second stage remain unclear. The ventral lateral geniculate nucleus (vLGN) is involved in the visual system and is shown to have complex origins from the thalamus, the zona limitans intrathalamica (ZLI) and the prethalamus. The transcription factor Pax6 is involved in the development of brain structures including the cortex, the diencephalon and the major axonal tracts in the forebrain by playing a multifaceted role in patterning, proliferation, differentiation, migration and axon guidance. It is known that Pax6 is essential in setting up the prosomeric boundaries in the developing diencephalon but its role in the formation of individual nuclei has not yet been explored. By using a conditional Pax6 knock-out mouse driven by Zic4Cre with a green fluorescent protein (GFP) reporter showing the Cre activity, the formation of the thalamic nuclei vLGN, dorsal lateral geniculate nucleus (dLGN) and VP (ventral posterior nuclei) was examined in postnatal day 0 (P0) Pax6+/+, Pax6fl/+ and Pax6fl/fl pups. Using this mouse model, I found an increase in nuclear volume at the rostral level and a global decrease in cell density in the P0 Pax6fl/fl vLGN, whereas in the dLGN an increase of GFP+ve cell proportion was observed. In Pax6fl/+, I found an increase in GFP+ve cell proportion in the caudal part of the vLGN and across the dLGN. No significant change was observed in the VP in either the Pax6fl/+ or the Pax6fl/fl. The defects in the vLGN and dLGN could be caused by: 1. disruption of the expression of patterning factors such as Shh and Nkx2.2; 2. cell proliferation defcts and abnormal apoptosis; 3. ocular developmental defects; 4. failure in cell sorting/migration; 5. cell fate change. During my PhD, I tested the first three theories and explored the fourth but was not able to pursue the last due to the time limit of the project. To test the hypothesized mechanisms underlying those defects seen in the vLGN and dLGN, I performed BrdU labelling to study the time origin of cells that contribute to these two nuclei and discovered that E11.5 and E12.5 are the main ages when these cells and the GFP+ve subpopulation are born. Then I carried out experiments to examine the cell proliferation and cell apoptosis in the thalamus (pTH-R, rostral part of the progenitor zone of the thalamus, and pTH-C, caudal part of the progenitor zone of the thalamus) and the prethalamus (Pth) from E11.5 to E13.5 and found: 1. the proliferation rate decreased in the pTH-R in Pax6fl/+ at E11.5; 2. the growth fraction decreased in both pTH-C and pTH-R in E12.5 Pax6fl/fl; 3. there is no change in cell proliferation in the GFP+ve subpopulation; 4. no abnormal apoptosis is observed in either the whole cell population or the GFP+ve subpopulation. Judging by the amplitude of the change in proliferation in the pTH-R and pTH-C at E11.5 and E12.5, it is unlikely that these changes alone are responsible for the phenotypes seen in P0 vLGN and dLGN. Then I examined the expression patterns of Shh and Nkx2.2 and the expansion of both was observed in Pax6fl/fl at both E12.5 and E13.5, which could explain the volume change of the vLGN but not the change in the proportion of GFP+ve subpopulation in both the vLGN and dLGN. Then I continued to examine if the ocular input from the retinal ganglionic cells are severely affected by the deletion of Pax6 and found no gross change in the conditional mutants, which rejected the ocular developmental defects theory. At the end of my PhD, I performed a BrdU short-term survival experiment and a brain slice culture combined with live imaging experiment to explore the possibility of abnormal cell migration causing the vLGN and dLGN phenotypes and found that the cells moving along the border of the thalamus and prethalamus move faster in the Pax6fl/fl than in the Pax6fl/+, but rather than moving directly toward the lateral surface of the diencephalon, they take a detour. These findings indicate that the deletion of Pax6 causes minor changes in the proliferation of E11.5 to E13.5 diencephalon and expansion of regional marker expression such as Shh and Nkx2.2, which could potenially affect the volume and change the proportion of GFP+ve cells in P0 vLGN and dLGN. Migration defects caused by Pax6 could also contribute to the phenotype observed in those two nuclei. Potential cell fate change caused by Pax6 deletion could be another factor that contributes to the defects in the conditional mutants. More work needs to be done to test the migration defect and cell fate change hypotheses in future.

In the visual system, retinal axons convey visual information from the outside world to dozens of distinct retinorecipient brain regions. In rodents, two major areas that are densely innervated by this retinal input are the dorsal lateral geniculate nucleus (dLGN) and ventral lateral geniculate nucleus (vLGN), both of which reside in the thalamus. The dLGN is well-studied and known to be important for classical image‐forming vision. The vLGN, on the other hand, is associated with non‐image‐forming vision and its neurochemistry, cytoarchitecture, and retinothalamic connectivity all remain unresolved, raising fundamental questions of its role within the visual system. Here, we sought to shed light on these important questions by studying the cellular and extracellular landscape of the vLGN and map its connectivity with the retina. Using bulk RNA sequencing and proteomics, we identified extracellular matrix proteins that form two molecularly distinct types of perineuronal nets in two major laminae of vLGN: the retinorecipient external vLGN (vLGNe) and the non‐retinorecipient internal vLGN. Using in situ hybridization, immunohistochemistry, electrophysiology, and genetic reporter lines, we found that vLGNe and vLGNi are also composed of diverse subtypes of neurons. In vLGNe, we discovered at least six transcriptionally distinct subtypes of inhibitory neurons that are distributed into distinct adjacent sublaminae. Using trans‐synaptic viral tracing and ex vivo electrophysiology, we found that cells in each these sublaminae receive direct inputs from retina. Lastly, by genetically removing visual input, we found that the organization of these sublaminae is dramatically disrupted, suggesting a crucial role for sensory input in the cytoarchitectural maintenance of the vLGN. Taken together, these results not only identify novel subtypes of vLGN cells, but they also point to new means of organizing visual information into parallel pathways – by anatomically creating distinct sensory channels. This subtype-specific organization may be key to understanding how the vLGN receives, processes, and transmits light‐derived signals in the subcortical visual system. / Doctor of Philosophy / As you look around, even as you read this abstract, your retinas are constantly taking in light, converting it into neural signals, and parsing it into different types of visual features. Those light-derived signals are then transmitted from the eye to dozens of brain areas through the optic nerve. Each of these brain areas is important for specialized visual functions. One of the most major visual areas is a region in the thalamus known as the ventral lateral geniculate nucleus (vLGN). Unlike the type of vision we typically think of which involves "seeing" an image, the vLGN primarily receives non-image-forming visual information from the eye which is important for a whole host of light-derived behaviors that do not involve image forming vision. These non-image-forming functions can impact things ranging from jet lag to eye movement to mood disorders and depression. Yet, despite the dense amount of visual information it receives, and the connections it has with many other brain regions, the vLGN has been largely understudied over the years, leaving many fundamental questions unanswered. Here, we unmasked the molecular and cellular landscape of the vLGN and discovered a rich and diverse set of neuronal cell types in this region. Further, by simultaneously labeling these neuronal types, we found that they stratify into their own layers, revealing a striking level of organization which suggests that the vLGN organizes visual information into parallel channels. These discoveries are important because understanding the composition and structure of the vLGN paves the way to understanding how it receives, processes, and transmits sensory signals in the visual system.

Retinogeniculate (RG) synapses connect retinal ganglion cells to the thalamic relay cells of the dorsal lateral geniculate nucleus (dLGN). They are critical for regulating the flow of visual information from retina to primary visual cortex (V1). RG synapses in dLGN are uniquely larger and stronger than their counterparts in other retinorecipient regions. Moreover, in dLGN, RG synapses can be classified into two groups: simple RG synapses, which contain glia-encapsulated single RTs synapsing onto relay cell dendrites, and complex RG synapses, which contain numerous RTs that converge onto the shared regions of relay cell dendrites. To identify target-derived molecules that direct the transformation of RTs into unique RG synapses in dLGN, I used RNAseq to obtain the whole transcriptome of dLGN and its adjacent retinorecipient nucleus, vLGN, at different time points during RG synapses development. Leucine-Rich Repeat Transmembrane Neuronal 1 (LRRTM1), a synaptogenic adhesion molecule, was the candidate I selected based on its expression pattern. Here, I discovered that LRRTM1 regulates the development of complex RG synapses. Mice lacking LRRTM1 (lrrtm1-/-) not only show a significant reduction in the number of complex RG synapses but they exhibit abnormal visual behaviors. This work reveals, for the first time, a high level of retinal convergence onto dLGN relay cells in thalamus and the functional significance of this convergence for vision. / Ph. D. / Our relationship with the environment is heavily reliant on vision, an intricately wired sensory system, much like a circuit. This circuit begins at the eyes, with the retina, and spreads to different visual centers in the brain. Retinal ganglion cells (RGCs) send their wires, called axons, carrying information about the visual world to over 40 different regions in the brain. A major target of these axons is the dorsal lateral geniculate nucleus (dLGN), a region critical to our ability to perceive the visual world. The sites where RGCs connect to the dLGN cells are called retinogeniculate (RG) synapses, and my studies focused on understanding how these RG synapses develop and how they function. I am the first to discover the fact that more than a dozen distinct RGC axons cluster within the same neighborhood of one shared target cell in the dLGN. Unique to the dLGN, these clusters, termed complex RG synapses, are not seen in any other RGC target regions in the brain. Moreover, I demonstrated a new molecular mechanism that forms these synapses by identifying a protein called LRRTM1, as a critical molecule required for the formation of these complex RG synapses in the dLGN. By studying the visual behavior of mutant mice lacking LRRTM1, I demonstrated that complex RG synapses are important for performing complex visual tasks. The discoveries detailed within this dissertation add to current efforts to restore vision in patients suffering from severe visual impairments, via regenerative therapies, by furthering our understanding of how neural wires connect in the visual circuit to reveal everything we will ever know about the visual world.

Vision provides a critical interface with the physical world. This work examines visual development and vision loss in mice to glean the influence of the retinal state on visual connections. I first assessed the impact of retinal activity on the eye-specific segregation of retinal afferents in the lateral geniculate nucleus (LGN) of young Gβ5 -/- mice. Gβ5 is the fifth member of the β subfamily of heterotrimeric G proteins. Gβ5 binds and stabilizes the R7 family of regulators of G-protein signaling (RGS), which accelerate Gi/o GTP hydrolysis. Gβ5 -/- mice, which lack R7RGS activity, have malformed synapses in the outer plexiform layer (OPL) and impaired OPL transmission. Altered spontaneous retinal activity in Gβ5-/- mice at P7, P12, P14, and P28 correlates with impaired eye-specific segregation of retinal afferents in the LGN at corresponding timepoints. However, Gβ5-/- mice exhibit a normal transition from cholinergic to glutamatergic drive that corresponds with a temporary recovery of refinement at P10. Thus the abnormal-normal-abnormal pattern of activity in the retina is coupled with abnormal-normal-abnormal segregation. This activity-segregation profile suggests activity may instruct early retinogeniculate development. nob mice, which also exhibit impaired OPL transmission, have aberrant retinal waves that align with loss of segregation. nobxGβ5-/- mice have similar levels of segregation as Gβ5-/- at P21, but activity only similar P14 nobxGβ5-/- and Gβ5-/- RGCs. This suggests that the critical period of eye-specific segregation closes shortly after P14 and that R7RGS activity is critically important to postnatal RGCs. Next, I investigated the aged visual system via the retinofugal projections of mice with retinal remodeling after photoreceptor degeneration (PD). ΔCT mice, with mild remodeling, and TG9N mice, with aggressive remodeling, retain gross anatomical and physiological connectivity in the presence of attenuated visual activity compounded by organic remodeling. However, the magnitude of pupillary light responses in PD mice was diminished. Reduced melanopsin signal in the retina, not downstream anomalies, explains this functional deficiency. These observations suggest that changes to eye-specific segregation are limited once projections are established, regardless of retinal activity or remodeling. These observations bode well for future retina-based treatments of vision loss.

In the mammalian visual system, the lateral geniculate nucleus is commonly thought to act merely as a relay for the transmission of visual information from the retina to the visual cortex, a relay without significant elaboration in receptive field properties or signal strength. However, many morphological and electrophysiological observations are at odds with this view. In this paper, we will review the different anatomical pathways and biophysical mechanisms possibly implementing a selective gating of visual information flow from the retina to the visual cortex. We will argue that the lateral geniculate nucleus in mammals is one of the earliest sites where selective, visual attention operates and where general changes in neuronal excitability as a function of the behavioral states of the animal, for instance, sleep, paradoxical sleep, arousal, etc., occur.

Axons of retinal ganglion cells (RGCs) send visual information to a number of retinorecipient regions in the brain. In rodents, visual thalamus receives dense innervations from RGC axons and is important for both image-forming and nonimage-forming visual functions. Retinal inputs invade visual thalamus during embryonic development, before the arrival of non-retinal inputs (such as local interneurons and axonal inputs from other brain regions). In this dissertation, I explore how early innervation of RGC axons affects circuitry in visual thalamus and the role of visual experience, neural activity, and molecular cues in the development. While the development of astrocytes in cortex has been well-described, they have been largely overlooked in visual thalamus. Using immunohistochemical, functional, and ultrastructural analysis, I show that astrocytes in visual thalamus reach adult-like morphological properties and functionality at retinogeniculate synapses early in development, by eye-opening and before visual experience. These studies reveal that while experience-dependent visual activity from RGC axons is critical for many aspects of visual thalamus development, astrocytic maturation occurs independent of that information about our visual environment. As with astrocytes, little progress has been made in understanding the development of interneurons in the visual thalamus. Here, I show that retinal inputs interact with thalamic astrocytes to influence the recruitment of GABAergic interneurons into visual thalamus. I found that this interaction between RGC axons and astrocytes is not dependent on neural activity of RGCs. Using transcriptomic analysis, in situ hybridization, and reporter lines, I observed thalamus-projecting RGCs express SHH and astrocytes in visual thalamus express SHH signaling molecules. My results reveal that SHH signaling between RGC axons and astrocytes is critical for astrocytic fibroblast growth factor 15 (FGF15) expression in developing visual thalamus. Ultimately, FGF15 serves as a potent motogen that is essential for thalamic interneuron migration. These data identify a novel morphogen-dependent and activity-independent mechanism that mediates crosstalk between RGCs and astrocytes to facilitate the recruitment of interneurons into the developing visual thalamus. / Doctor of Philosophy / The most dominant sense in human is the sight, which we need to interact with our environment efficiently. The retina takes up the information about our visual world and sends it to the brain, which ultimately puts everything together, for us to see properly. The visual information from the retina goes to the brain via nerves (which are essentially cables/wires of brain cells). These nerves from the retina go to many places in the brain, including a region called visual thalamus, which is the focus of my PhD work. For the past five years, I have been trying to understanding if nerves from the retina play a role in the brain formation during early development. To study this, I have used mice as a model system, as their brain regions that process visual information have very similar structural architecture to those in humans. My research shows that retinal nerves are indeed important for the development of visual thalamus. Here, I show that information from the eye is critical for migration (a process during development where brain cells move from their place of origin to their final location) of cells in visual thalamus. Discoveries made in this dissertation are important because they highlight how different cells in the central nervous system communicate with each other at the level of molecules and how these interactions are important for building circuits that are important for vision.

In the developing visual system, the axon of a pre-synaptic cell must be guided to a post-synaptic partner. Retinal ganglion cells (RGCs) in the eye are an excellent model to study this process. Multiple classes exist that respond to specific types of light input, and these project to different destinations in the brain that process distinct types of information. The RGC axons that navigate to the lateral geniculate nucleus (LGN) do so in a class-specific manner. Axons from RGCs that mediate non-image forming functions innervate the ventral LGN (vLGN) and the intergeniculate leaflet (IGL). Axons from RGCs that process image-forming information bypass these regions to innervate the dorsal LGN (dLGN). The extracellular protein reelin was identified as a potential factor in RGC axonal targeting of the vLGN and IGL, and the reeler mutant mouse used to study the effects of its functional absence. Anterograde labeling of RGCs and their axons with Cholera toxin B (CTB) revealed reduced patterns of retinal innervation to the vLGN and IGL in mutant mice. Moreover, the absence of functional reelin resulted in axons incorrectly growing into inappropriate regions of the thalamus. We identified these misrouted axons as those of the intrinsically photosensitive RGCs (ipRGCS), a class of RGCs known to project to the affected subnuclei. In contrast to defects in ipRGC targeting, no deficits were seen in retinogeniculate or corticothalamic projections in classes of axons that normally target the dLGN. Immunohistochemistry did not reveal any effects of the absence of the functional reelin on the LGN cytoarchitecture, which is unlike many other brain regions altered in the reeler. In summary, results suggest that intact reelin is required for class-specific retinogeniculate targeting to the vLGN and IGL. The defects are likely to be in targeting and not in neuronal positioning.

Visual sub-modalities, such as colour, form and motion perception, are analysed in parallel by three visual “pathways” – the parvocellular (PC), magnocellular (MC) and koniocellular (KC) pathways. This thesis aims to further elucidate some properties of the subcortical pathways for colour vision. The experimental animal used throughout is a New World monkey, the common marmoset Callithrix jacchus. (For complete abstract open document)

The primate visual system is organised and wired in a topological manner. From the eye well into extrastriate visual cortex, a preserved spatial representation of the vi- sual world is maintained across many levels of processing. Diffusion-weighted imaging (DWI), together with probabilistic tractography, is a non-invasive technique for map- ping connectivity within the brain. In this thesis I probed the sensitivity and accuracy of DWI and probabilistic tractography by quantifying its capacity to detect topolog- ical connectivity in the post mortem macaque brain, between the lateral geniculate nucleus (LGN) and primary visual cortex (V1). The results were validated against electrophysiological and histological data from previous studies. Using the methodol- ogy developed in this thesis, it was possible to segment the LGN reliably into distinct subregions based on its structural connectivity to different parts of the visual field represented in V1. Quantitative differences in connectivity from magno- and parvo- cellular subcomponents of the LGN to different parts of V1 could be replicated with this method in post mortem brains. The topological corticocortical connectivity be- tween extrastriate visual area V5/MT and V1 could also be mapped in the post mortem macaque. In vivo DWI scans previously obtained from the same brains have lower resolution and signal-to-noise because of the shorter scan times. Nevertheless, in many cases, these yielded topological maps similar to the post mortem maps. These results indicate that the preserved topology of connection between LGN to V1, and V5/MT to V1, can be revealed using non-invasive measures of diffusion-weighted imaging and tractography in vivo. In a preliminary investigation using Human Connectome data obtained in vivo, I was not able to segment the retinotopic map in LGN based on con- nections to V1. This may be because information about the topological connectivity is not carried in the much lower resolution human diffusion data, or because of other methodological limitations. I also investigated the mechanisms of perceptual learning by developing a novel task-irrelevant perceptual learning paradigm designed to adapt neuronal elements early on in visual processing in a certain region of the visual field. There is evidence, although not clear-cut, to suggest that the paradigm elicits task- irrelevant perceptual learning, but that these effects only emerge when practice-related effects are accounted for. When orientation and location specific effects on perceptual performance are examined, the largest improvement occurs at the trained location, however, there is also significant improvement at one other 'untrained' location, and there is also a significant improvement in performance for a control group that did not receive any training at any location. The work highlights inherent difficulties in inves- tigating perceptual learning, which relate to the fact that learning likely takes place at both lower and higher levels of processing, however, the paradigm provides a good starting point for comprehensively investigating the complex mechanisms underlying perceptual learning.

The ability to read proficiently is key to social participation and an important premise for individual well-being and vocational success. Individuals with developmental dyslexia, a highly prevalent neurodevelopmental disorder affecting hundreds of millions of children and adults worldwide, face severe and persistent difficulties in attaining adequate reading levels. Despite years of extensive research efforts to elucidate the neurobiological origin of this disorder, its exact etiology remains unclear to date. In this context, most neuroimaging research on dyslexia in humans has focused on the cerebral cortex and has identified alterations in a distributed left-lateralized cortical language network. However, pioneering post-mortem human studies and animal models suggest that dyslexia might also be associated with alterations in subcortical sensory thalami and early sensory pathways. The largely cortico-centric view of dyslexia is due in part to considerable technical challenges in assessing the human sensory thalami non-invasively using conventional magnetic resonance imaging (MRI). As a result, the role that sensory thalami may play in dyslexia has been largely unaddressed. In this dissertation, I leveraged recent advances in high-field MRI to investigate the role of the human lateral geniculate nucleus (LGN) of the visual thalamus in adults with dyslexia in-vivo. In three multi-modal high-field MRI studies, I show that (i) dyslexia is associated with structural alterations in the direct V1-bypassing white matter pathway connecting the LGN with cortical motion-sensitive area V5/MT in the left hemisphere; (ii) the connectivity strength of which predicts a core symptom of the disorder, i.e., rapid naming ability. I further demonstrate that (iii) the two major functional subdivisions of the LGN can be distinguished non-invasively based on differences in tissue microstructure; and that (iv) adults with dyslexia show functional response alterations specifically in the magnocellular subdivision of the LGN. I also demonstrate that this subdivision deficit (v) is more pronounced in male than female dyslexics; and (vi) predicts rapid naming ability in male dyslexics only. The results of this doctoral thesis are the first to confirm previous post-mortem evidence of LGN alterations in dyslexia in-vivo and point to their relevance to key symptoms of the disorder. In synergy, our research findings offer new perspectives on explanatory models of dyslexia and bear potential implications also for prospective treatment strategies.:Contribution Statement i Acknowledgments iii Abstract v Table of Contents vii 1 General Introduction 1 1.1 Developmental Dyslexia 1 1.1.1 Diagnostic Criteria 1 1.1.2 Prevalence and Etiology 2 1.1.3 Cognitive and Behavioral Symptoms 3 1.1.4 Explanatory Models in Cognitive Neuroscience 4 1.2 Lateral Geniculate Nucleus 7 1.2.1 Anatomy and Function 7 1.2.2 Technical Challenges in Conventional MRI 8 1.2.3 High-Field MRI 9 1.3 Research Aim and Chapter Outline 10 2 Altered Structural Connectivity of the Left Visual Thalamus in Developmental Dyslexia 13 2.1 Summary 14 2.2 Results and Discussion 15 2.3 Conclusions 22 2.4 Materials and Methods 23 2.4.1 Subject Details 23 2.4.2 High-Resolution MRI Acquisition and Preprocessing 23 2.4.3 Lateral Geniculate Nucleus Definition 24 2.4.4 Cortical Region of Interest Definition 26 2.4.5 Probabilistic Tractography 27 2.4.6 Quantification and Statistical Analysis 29 2.5 Supplementary Information 30 3 Mapping the Human Lateral Geniculate Nucleus and its Cytoarchitectonic Subdivisions Using Quantitative MRI 33 3.1 Abstract 34 3.2 Introduction 35 3.3 Materials and Methods 37 3.3.1 In-Vivo MRI 37 3.3.2 Post-Mortem MRI and Histology 41 3.4 Results 44 3.4.1 Lateral Geniculate Nucleus Subdivisions in In-Vivo MRI 44 3.4.2 Lateral Geniculate Nucleus Subdivisions in Post-Mortem MRI 46 3.5 Discussion 50 3.6 Supplementary Information 54 3.6.1 In-Vivo MRI 54 3.6.2 Post-Mortem MRI and Histology 58 3.6.3 Data and Code Availability 60 4 Dysfunction of the Visual Sensory Thalamus in Developmental Dyslexia 61 4.1 Abstract 62 4.2 Introduction 63 4.3 Materials and Methods 66 4.3.1 Subject Details 66 4.3.2 High-Resolution MRI Experiments 66 4.3.3 High-Resolution MRI Acquisition and Preprocessing 67 4.3.4 Lateral Geniculate Nucleus Definition 68 4.3.5 Quantification and Statistical Analysis 69 4.4 Results 70 4.5 Discussion 75 4.6 Supplementary Information 77 4.6.1 Supporting Methods 77 4.6.2 Supporting Results 81 4.6.3 Data and Code Availability 82 5 General Conclusion 83 5.1 Summary of Research Findings 83 5.2 Implications for Dyslexia Models 84 5.2.1 Phonological Deficit Hypothesis 84 5.2.2 Magnocellular Theory 84 5.2.3 Model According to Ramus 85 5.2.4 Need for Revised Model 86 5.3 Implications for Remediation 87 5.4 Research Prospects 88 5.5 Brief Concluding Remarks 90 6 Bibliography 91 7 List of Tables 113 8 List of Figures 115 9 Selbstständigkeitserklärung 117