<p>Despite a largely static DNA sequence, our genomes are incredibly malleable. Comparative studies of chromatin features between different cell types, tissues, and species have revealed tremendous differences in how the genome is accessed, transcribed, and replicated. However, how the dynamics of chromatin accessibility contribute to development, environmental response, and disease status has only begun to be appreciated. In this work we identified chromatin accessibility changes by DNase-seq in three diverse processes: in granule neurons of the developing cerebellum, with intestinal epithelial cells in the absence of a normal microbiota, and with myelogenous leukemia cells in response to histone deacetylase inhibitor treatments. In all cases, we coupled these analyses with RNA-seq assays to identify concurrent transcriptional changes. By mapping the changes to these genome-wide signals we defined the contribution of local chromatin structure to the transcriptional programs underlying these processes, and improved our understanding of their relation to other chromatin changes like histone modifications. Furthermore we demonstrated use of the strongest accessibility changes to identify transcription factors critical for these processes by finding enrichment of their binding motifs. For a few of these key factors, depletion or overexpression of the protein was sufficient to regulate the expression of predicted target genes or exert limited chromatin accessibility changes, demonstrating the functional significance of these proteins in these processes. Together these studies have informed our understanding of the role chromatin accessibility changes play in development and environmental responses while also proving their utility for key regulator identification.</p> / Dissertation

The voltage-gated potassium channel Kv1.2 impacts membrane potential and therefore excitability of neurons. Expression of Kv1.2 at the plasma membrane (PM) is critical for channel function, and altering Kv1.2 at the PM is one way to affect membrane excitability. Such is the case in the cerebellum, a portion of the brain with dense Kv1.2 expression, where modulation of Kv1.2 at the PM can impact electrical activity of neurons and ultimately cerebellum-dependent learning. Modulation of Kv1.2 at the PM can occur through endocytic trafficking of the channel; however mechanisms behind this process in the brain remain to be defined. The goal of this dissertation was to identify and characterize modalities endogenous to the brain that influence the presence of Kv1.2 at the neuronal plasma membrane. Mass spectrometry (MS) was used to first identify interacting proteins and post-translational modifications (PTM) of Kv1.2 from cerebellar tissue, and the roles of these interactions and modifications on Kv1.2 function were evaluated in two studies: The first study investigated Trim32, a protein enzyme that catalyzes ubiquitylation, a PTM involved in protein degradation, but also in non-degradative events such as endocytic trafficking. Trim32 was demonstrated to associate and localize with Kv1.2 in cerebellar neurons by MS, immunoblotting (IB), and immunofluorescence (IF), and also demonstrated the ability to ubiquitylate Kv1.2 in vitro through purified recombinant proteins. Utilizing cultured cells through a combination of mutagenesis, biochemistry, and quantitative MS, a working model of Kv1.2 modulation was developed in which Trim32 influences Kv1.2 surface expression by two mechanisms that both involve cross-talk of ubiquitylation and phosphorylation sites of Kv1.2. The second study investigated WNK1, a chloride-sensitive kinase which regulates cellular homeostasis. Using MS, IB, and IF, WNK1 was demonstrated to associate and localize with Kv1.2 in the cerebellum, and a combination of mutagenesis and pharmacology in both wild-type and WNK1-knockout cultured cells produced a working model whereby WNK1 modulates surface Kv1.2. Activation of the downstream target SPAK kinase, also identified by MS to associate with Kv1.2 in the brain, by WNK1 was additionally found to influence the manner of WNK1 modulation of Kv1.2. In addition to providing new models of Kv1.2 modulation in the brain, these studies propose novel biological roles for Trim32 and WNK1 that may ultimately impact neuronal excitability.

Dans le cortex cérébelleux, au premier chef impliqué dans l’apprentissage moteur, chaque neurone de Purkinje reçoit des centaines de milliers d'entrées provenant de cellules granulaires. Etonnement, il a été suggéré qu'une grande majorité de ces connexions (synapses) sont silencieuses, c’est-à-dire qu’elles ne transmettent pas d’information détectable. Les propriétés et le rôle de ces synapses silencieuses restent mystérieux. Jouent-elles le rôle d’une réserve ou sont-elles le produit de l’apprentissage cérébelleux ? En combinant l’enregistrement électrique de la transmission synaptique et la cartographie des entrées synaptiques dans des tranches aigües de cervelet de souris, nous avons étudié l'évolution du pourcentage des synapses qui sont silencieuses entre deux âges : avant le sevrage et une fois que l’agilité d’adulte est acquise. Nous avons observé que le pourcentage de synapses qui sont silencieuses reste remarquablement stable malgré l’augmentation du nombre total de synapses. / In the cerebellar cortex, primarily involved in motor learning, any Purkinje neuron receives hundreds of thousands of inputs from granule cells. Disturbingly, it has been suggested that the vast majority of these connections (synapses) are silent, that is to say they do not transmit any detectable information. The properties and the role of these silent synapses remains mysterious. Do they serve as a reserve pool for additional information storage or are they a byproduct of cerebellar learning? Combining the electrical recording of synaptic transmission and the mapping of synaptic inputs in acute cerebellar slices from mice, we have studied how the percentage of synapses which are silent changes between two postnatal ages: before weaning and once adult agility is acquired. Our main finding is that the percentage of synapses which are silent remains remarkably stable despite the increase in the total number of synapses.

The developing brain requires an intricate network of signals to direct proliferation, differentiation and cell fate decisions. Primary cilia are vital organelles with an emerging role regulating several major signalling cascades, in particular the Hedgehog pathway. Talpid3 (Ta3) is 166.7 kD protein found at the distal tip of centrioles. It has been shown to interact with a number of key centriolar proteins and is essential for the formation of primary cilia. A recent mouse model has been designed to conditionally target the highly conserved coiled-coil domain of Ta3 using the Cre/loxP system. This project uncovers the role of Ta3 in the developing brain. It characterises in detail the phenotype of mice with conditional loss of Ta3 in the central nervous system using the Nestin-Cre deleter strain. Morphological and histological analyses demonstrate that significant defects occur postnatally with mice developing severe ataxia and hydrocephaly. Immunohistochemical techniques further characterise the distinct phenotypes of three key brain regions including the cerebellum, cortex and hippocampus. Ta3fl/fl;NesCre mutant mice exhibit defects in the proliferation, organisation, morphology and migration of both neuronal and glial cells. We have shown the mechanistic cause to be the result of widespread loss of primary cilia and a concomitant disruption in the transduction of the Hedgehog signalling pathway. The neural roles of Ta3 are explored further through the optimisation of an in vitro neurosphere system to culture postnatal hippocampal progenitors. The use of a tamoxifen inducible strain allows the timely recombination of Ta3 to study its role in a controlled environment. The cultured cells recapitulate many of the in vivo defects showing loss of primary cilia and reduced migration. Finally, characterisation of the phenotypes seen in the Ta3fl/fl;NesCre mice were shown to resemble neurological traits seen in human conditions with loss of Primary cilia, known as ‘human ciliopathies’. Through clinical collaboration this project demonstrated a human ciliopathy case of Joubert Syndrome with compound heterozygous mutations in TA3. This presents the Ta3fl/fl;NesCre mutant mice as a valuable model system to study a rare but clinically relevant condition.

Forkhead domain基因家族編碼了很多對於胚胎發育至關重要的轉錄因子，而Foxp4則屬於p-subtype forkhead轉錄因子其中一員。Foxp4在胚胎發育期間的表達十分活躍，在發育中的腦部的不同地方表達，但其於中樞神經系統發育中的調控角色並不清楚。Foxp4基因剔除小鼠在出生前死於心臟的缺陷表型(心二分支) ，在此時間段，腦部的發育才剛剛開始，因此我們無法利用Foxp4基因剔除小鼠作為研究中樞神經系統發育的動物模型。最近，我們的團隊利用小腦組織培養技術及siRNA發佈的研究顯示，Foxp4在小鼠小腦中的蒲金氏細胞(Purkinje cell)中擔當著重要的維持作用。這項研究結果加深了我們對研究Foxp4在中樞神經系統發育中的調控角色的決心。 / 本論文旨在利用斑馬魚作為實驗模型，研究foxp4在斑馬魚中樞神經系統發育中的表達及調控角色。RT-PCR結果顯示foxp4在斑馬魚發育中的bud stage開始表達，並在及後的階段維持其表達水平。利用原位雜交技術 (whole mount in-situ hybridization)，我們發現foxp4表達的地區主要集中於發育中的腦部。在成年斑馬魚中，foxp4表達在不同組織和器官，包括腦部，眼睛和心臟。成年斑馬魚腦部切片原位雜交 (sectioned in-situ hybridization)則顯示，foxp4在小腦的蒲金氏細胞和視頂蓋(optic tectum)的periventricular gray zone表達。 / 為了進一步探究foxp4對於胚胎發育過程中的功能，我們利用微注射技術，把反義嗎啉 (morpholino) MO1注射到斑馬魚胚胎中，大幅度抑制foxp4的表達水平。胚胎受精後48小時，MO1注入的胚胎顯示出第四腦室腦積水的缺陷表型。組織學分析顯示，第四腦室以下的延髓被壓縮致形態異常。此外，利用原位雜交技術及不同的分子標記，我們發現胚胎的中後腦邊界也會出現輕度畸形，而後腦的神經元數量及排列亦受到影響。 / 本項研究展示foxp4在胚胎中樞神經系統的發展的重要性，亦提供了新的見解。我們認為foxp4可能是調控腦室發育的重要成員，但在此方面與foxp4相關的分子機制仍須作更深入的研究。 / The forkhead domain gene family encodes a large group of transcription factors that play essential roles in development. Foxp4 is one of the members in the Foxp subfamily that expressed in different parts of developing central nervous system (CNS) and its function is less characterized. Previous study on Foxp4-knockout mice resulted in early embryonic lethality due to defective heart tube development that hindered the functional study of Foxp4 in CNS development. Recently, our laboratory reported that Foxp4 functions as a maintenance role in the Purkinje cell in the mouse cerebellum. Nevertheless, the role of foxp4 in CNS development was still unclear. / In this study, we used zebrafish as a model to study the expression pattern and functional study of foxp4 in the developing CNS. RT-PCR analysis showed that foxp4 transcript was expressed at the bud stage and maintained in the later embryonic stages. Whole-mount in-situ hybridization showed that foxp4 expressed in the cephalic region during embryonic development. In adult zebrafish, foxp4 expresses in different tissues and organs including brain, eye and heart. Sectioned in-situ hybridization of the adult zebrafish brain showed that foxp4 was specifically expressed in the Purkinje cell and the periventricular gray zone of optic tectum. / To further investigate the function of foxp4 during embryonic development, we injected antisense morpholino, MO1 into the zebrafish embryo to knockdown foxp4. By 48 hour post fertilization (hpf), MO1-injected embryos displayed hydrocephalus in the 4th ventricle. Histological analysis revealed that the medulla oblongata below the 4th ventricle was compressed by the edema resulting in abnormal morphology of medulla oblongata in the MO1-injected morphant. In addition, a mild malformation of the mid-hindbrain boundary, disrupted hindbrain patterning was observed in MO1-injected morphant. / Our findings provide new insight into the function of foxp4 in embryonic CNS development. We suggested that foxp4 may be essential in regulating the brain ventricle development while the molecular mechanism underlying the functional role of foxp4 requires further investigation. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Wong, Wai Kei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 92-102). / Abstracts also in Chinese. / Abstract --- p.iii / 摘要 --- p.v / Acknowledgement --- p.vii / Figure and table list --- p.xi / Abbreviation --- p.xii / Chapter Chapter 1 --- General Introduction / Chapter 1.1 --- Zebrafish as a developmental model --- p.1 / Chapter 1.2 --- Zebrafish development with highlights --- p.3 / Chapter 1.2.1 --- CNS development --- p.3 / Chapter 1.3 --- Forkhead domain gene in development --- p.5 / Chapter 1.3.1 --- History of forkhead domain gene --- p.5 / Chapter 1.3.2 --- Functional roles of forkhead domain genes in development --- p.6 / Chapter 1.4 --- Foxp subfamily --- p.8 / Chapter 1.4.1 --- Diverse functions of Foxp1, 2, 3 and 4 --- p.8 / Chapter 1.4.2 --- Relationship between Foxp subfamily members --- p.10 / Chapter 1.5 --- Foxp4 --- p.11 / Chapter 1.5.1 --- Genomic organization and protein structure of mFoxp4 --- p.11 / Chapter 1.5.2 --- Previous studies of mFoxp4 --- p.14 / Chapter 1.5.3 --- Foxp4 studies in other model organisms --- p.14 / Chapter 1.5.3.1 --- Rat --- p.15 / Chapter 1.5.3.2 --- Xenopus --- p.16 / Chapter 1.5.3.3 --- C. elegans --- p.16 / Chapter 1.5.4 --- Zebrafish foxp4 --- p.17 / Chapter 1.5.5.1 --- Genomic organization and protein structure of foxp4 --- p.17 / Chapter 1.5.5.2 --- Sequence alignment of foxp4 with other models --- p.19 / Chapter 1.6 --- Hypothesis, aim and strategy of the study --- p.22 / Chapter Chapter 2 --- Expression of foxp4 in zebrafish embryo and adult zebrafish brain / Chapter 2.1 --- Introduction --- p.24 / Chapter 2.2 --- Materials and methods --- p.25 / Chapter 2.2.1 --- Animals --- p.25 / Chapter 2.2.2 --- Materials --- p.26 / Chapter 2.2.3 --- Semi-quantitative PCR --- p.35 / Chapter 2.2.3.1 --- cDNA of zebrafish embryo --- p.35 / Chapter 2.2.3.2 --- Isolation of adult zebrafish organs --- p.36 / Chapter 2.2.3.3 --- RNA extraction and reverse transcription --- p.36 / Chapter 2.2.3.4 --- Polymerase chain reaction --- p.37 / Chapter 2.2.4 --- Subcloning of DNA fragment / Chapter 2.2.4.1 --- Preparation of cloning vectors --- p.40 / Chapter 2.2.4.2 --- Subcloning of DNA fragments --- p.40 / Chapter 2.2.4.3 --- Transformation of DNA into competent cells --- p.40 / Chapter 2.2.4.4 --- Preparation of recombinant plasmid DNA --- p.41 / Chapter 2.2.5 --- Whole mount in-situ hybridization of zebrafish embryo --- p.45 / Chapter 2.2.5.1 --- Preparation of equipment --- p.45 / Chapter 2.2.5.2 --- Preparation of zebrafish embryos --- p.45 / Chapter 2.2.5.3 --- Preparation of RNA probe --- p.46 / Chapter 2.2.5.4 --- Whole-mount in-situ hybridization --- p.48 / Chapter 2.2.6 --- Sectioned in-situ hybridization of adult zebrafish brain --- p.49 / Chapter 2.2.6.1 --- Histology of adult zebrafish brain --- p.49 / Chapter 2.2.6.2 --- Sectioned in-situ hybridization --- p.50 / Chapter 2.3 --- Results --- p.51 / Chapter 2.3.1 --- Expression profile of foxp4 in different stages of zebrafish embryo --- p.51 / Chapter 2.3.2 --- Expression pattern of foxp4 in different stages of zebrafish embryo --- p.54 / Chapter 2.3.3 --- Expression profile of foxp4 in different zebrafish organs and tissues --- p.57 / Chapter 2.3.4 --- Expression pattern of foxp4 in adult zebrafish brain --- p.59 / Chapter 3.4 --- Discussion --- p.61 / Chapter Chapter 3 --- Functional analysis of foxp4 in zebrafish embryonic development / Chapter 3.1 --- Introduction --- p.63 / Chapter 3.2 --- Materials and methods --- p.64 / Chapter 3.2.1 --- Materials --- p.64 / Chapter 3.2.2 --- Design of morpholino --- p.68 / Chapter 3.2.3 --- Sequencing of morpholino target regions of foxp4 --- p.70 / Chapter 3.2.4 --- Microinjection --- p.70 / Chapter 3.2.4.1 --- Preparation of materials and equipment --- p.70 / Chapter 3.2.4.2 --- Preparation of injection needle --- p.70 / Chapter 3.2.4.3 --- Preparation of morpholinos --- p.70 / Chapter 3.2.4.4 --- Calibration of injection volume --- p.71 / Chapter 3.2.4.5 --- Microinjection of zebrafish embryo --- p.71 / Chapter 3.2.5 --- Western blotting to assay foxp4 translation inhibition --- p.72 / Chapter 3.2.5.1 --- Preparation of protein extracts --- p.72 / Chapter 3.2.5.2 --- Coomassie blue staining --- p.73 / Chapter 3.2.5.3 --- Western blotting --- p.74 / Chapter 3.2.6 --- Whole mount in-situ hybridization --- p.74 / Chapter 3.3 --- Results --- p.75 / Chapter 3.3.1 --- MO1 knockdown efficiency assayed by Western blotting --- p.75 / Chapter 3.3.2 --- General morphology of morphants --- p.77 / Chapter 3.3.3 --- Histology at the hindbrain region showing the phenotype --- p.79 / Chapter 3.3.4 --- Whole mount in-situ hybridization of different molecular markers --- p.81 / Chapter 3.4 --- Discussion --- p.85 / Chapter Chapter 4 --- Future directions and conclusion / Chapter 4.1 --- Future directions --- p.89 / Chapter 4.2 --- Conclusion --- p.91 / Reference --- p.92

Chronic neck pain, including subclinical neck pain (SCNP), is a significant problem that places a burden on the healthcare system. Chiropractic manipulation has shown not only to be effective in treating symptoms of neck pain, but also in providing a neuromodulatory effect on the central nervous system. The motor cortex and cerebellum are thought to be important neural structures involved in motor learning and sensorimotor integration (SMI), and are therefore key structures to investigate how SMI is changed in a SCNP group following chiropractic care. Motor sequence learning (MSL) has also been shown to provide alterations in cerebellar projections to the motor cortex. Therefore, the studies in this thesis set out to determine if it was possible to induce both cortical and cerebellar learning, and if chiropractic care could alter motor output via transcranial magnetic stimulation measures to facilitate this learning. The study‟s results suggest that in a healthy group of subjects there is alteration in the intracortical inhibition of the motor cortex and no significant change in the cerebellum, following MSL. However, the results also suggest that in a SCNP group, there is a modulation of the cerebellar connections to the motor cortex but no effect specific to the motor cortex following both MSL and chiropractic manipulation. Therefore, these findings suggest that people with intermittent neck pain have concomitant changes in SMI and could manifest as clinical symptomology. / UOIT

The vestibulo-ocular reflex (VOR) is a simple reflex that stabilizes gaze by moving the eyes in the opposite direction to the head. The gain of the VOR (ratio of head to eye velocity) can be increased or decreased during motor learning. It is thought that the memory for learned changes in the VOR gain is initially encoded within the cerebellar flocculus. Furthermore, these learned gain changes can be disrupted or consolidated into a long-term memory. In this thesis we describe novel results that show that consolidation of the VOR can take place rapidly, within 1 hour after learning has stopped. Furthermore, we demonstrated that unlike learning, which has been shown to have frequency selectivity, disruption and rapid consolidation generalize across the range of frequencies. We suggest that disruption and rapid consolidation in the VOR are local mechanisms within the cerebellar cortex, and do not require new learning. This thesis also provides additional evidence for the idea that learned gain increases and decreases are the result of separate mechanisms, most likely long-term depression and potentiation respectively, at the parallel fibre-Purkinje cell synapses. We demonstrate that learned gain increases, but not decreases, require the activation of type 1 metabotropic glutamate receptors (mGluR1) and B type γ-aminobutyric acid (GABAB) receptors. Blocking one or both of these receptors with an antagonist inverts gain-up learning, while the agonist augments gain-up learning. Furthermore, we provide novel evidence that these receptors are co-activated during gain-up learning.

The vestibulo-ocular reflex (VOR) is a simple reflex that stabilizes gaze by moving the eyes in the opposite direction to the head. The gain of the VOR (ratio of head to eye velocity) can be increased or decreased during motor learning. It is thought that the memory for learned changes in the VOR gain is initially encoded within the cerebellar flocculus. Furthermore, these learned gain changes can be disrupted or consolidated into a long-term memory. In this thesis we describe novel results that show that consolidation of the VOR can take place rapidly, within 1 hour after learning has stopped. Furthermore, we demonstrated that unlike learning, which has been shown to have frequency selectivity, disruption and rapid consolidation generalize across the range of frequencies. We suggest that disruption and rapid consolidation in the VOR are local mechanisms within the cerebellar cortex, and do not require new learning. This thesis also provides additional evidence for the idea that learned gain increases and decreases are the result of separate mechanisms, most likely long-term depression and potentiation respectively, at the parallel fibre-Purkinje cell synapses. We demonstrate that learned gain increases, but not decreases, require the activation of type 1 metabotropic glutamate receptors (mGluR1) and B type γ-aminobutyric acid (GABAB) receptors. Blocking one or both of these receptors with an antagonist inverts gain-up learning, while the agonist augments gain-up learning. Furthermore, we provide novel evidence that these receptors are co-activated during gain-up learning.

No description available.

The third ventricle region houses several neuroanatomical structures that are primary components of the human memory system, and provides pathways through which these brain regions communicate with critical regions of the frontal and medial temporal lobes. Archival data was obtained for 42 children with cerebellar or third ventricle tumors, and was examined for tumor and treatment related confounds. Children with third ventricle tumors were hypothesized to exhibit; 1) better performance on a measure of auditory attention, 2) greater impairment in learning across trials, 3) greater memory loss over a 20-minute delay, and 4) greater impairment across delayed memory tests than the cerebellar group. Children with third ventricle tumors demonstrated significantly better auditory attention, but greater impairments in verbal learning, and greater verbal memory loss following a 20-minute delay. In contrast, children with third ventricle tumors did not demonstrate significantly greater memory impairments across long delay memory tests.