No description available.

Cilia are polarized extensions of the cells microtubule-based cytoskeleton dedicated to sensory, signaling and motility-related functions. In mammals, there are two main types of cilia, immotile and motile, where motile cilia generate/modulate fluid flow at the embryonic node, in respiratory airways, cerebral ventricles and the oviduct in addition to sperm propulsion via the flagellum. Defects in cilia motility cause a rare genetic disorder called Primary Ciliary Dyskinesia (PCD). In this thesis, I present functional and molecular characterisation of two PCD causing genes HEATR2 and ZMYND10. Core cilia genes are transcriptionally activated by members of the winged-helix transcription factors of the RFX family. The forkhead transcription factor FOXJ1, additionally activates motility genes such as the ones encoding components of axonemal dynein motors which transfer the chemical energy released from ATP hydrolysis to kinetic motion necessary for ciliary motility. I present data in this thesis which show that Heatr2 and Zmynd10 are both targets of the RFX3-FOXJ1 transcriptional module which co-operatively switches on genes required to make motile cilia Mutations in both HEATR2 and ZMYND10 cause the same subtype of PCD (loss of inner and outer arm dyneins in cilia). I characterise a human PCD causing mutation in HEATR2 in this thesis. Additionally, using genetic null mouse models generated using the CRISPR technology, I describe the phenotypic effects of complete loss of Zmynd10 in mice. Zmynd10 mutant mice display characteristic PCD-like features. Adding to my functional studies, I present proteomic data to propose mechanisms by which HEATR2 and ZMYND10 proteins control cilia motility. Mass spectrometry and protein interaction studies support distinct roles for HEATR2 and ZMYND10 in intracellular transport and pre-assembly of axonemal dynein motors. The multisystem approaches described in this thesis to characterise the roles of HEATR2 and ZMYND10 highlight the molecular complexity underlying the assembly and delivery of axonemal dyneins to motile cilia and provide novel functional and molecular insights into the pathophysiology of PCD.

Purpose: Sperm nuclear proteins and DNA integrity have been implicated in infertility and treatment failures. High stallion to stallion variability is observed in sperm cryopreservation protocols. The cells are destroyed with harsh chemicals prior to using biochemical assays to test sperm DNA quality. The feasibility of using Raman spectrometry in combination with a laser trap for non-destructive micromanipulation and characterization of DNA damage in motile stallion and human sperm is experimentally investigated in this thesis. Methods: Live stallion sperms were subjected to controlled cellular damage: (a) four grades of chemically induced oxidative stress using Xanthine – Xanthine Oxidase (b) three grades of osmotic stress using PBS and (c) membrane damage using thermal shock. Live human sperm DNA disintegration with time and oxidative stress were explored on fresh, cryopreserved and swim-up categories. The specimens ranged from sub-fertile patients to fertile donors in a limited study. Post-treatment sperms resuspended in sperm media, placed on a quartz coverslip were trapped with a 785 nm, 25 mW laser, using a 1.4 NA, 60X, water immersion microscope objective. A Raman spectrum of a trapped cell was acquired for 20 – 30 seconds. The spectra from 20 – 40 cells from each specimen were analysed in the 630 cm-1 – 1630 cm-1 region using statistical variance and PCA. Results: The Raman spectra from trapped motile sperm head contain intense peaks that did not require smoothing prior to analysis. PCA of the Raman spectra could not resolve the different grades of applied osmotic and oxidative stress in stallion cells. PCA showed high variability between specimens from the same stallion and between stallions, with distinct clustering by ejaculate. Membrane damage study and spectra from extended trapping also showed distinct specimen to specimen difference within and between stallions. Specimen to specimen variability is observed in motility and viability tests on 1000s of stallion cells using CASA and flow cytometry. Human sperms showed some clustering by category, time, stress and motility and appeared more sensitive to the tests than stallion sperms. Conclusions: Raman spectra originate from the dense region of the trapped sperm head and resemble the fingerprint of dense calf thymus DNA. The cells show species specific response to the applied stress/damage. Stallion sperms show high variability between ejaculates that could not be differentiated by stallions. Human cells appear more sensitive to the applied processes. LTRS of live sperms needs further detailed research, cross correlated with other established complementary techniques, to identify spectral bands that are most sensitive to the various grades of induced DNA and membrane damage.

During embryogenesis, airway epithelial cells possess primary cilia, and HH signaling guides lung development. As epithelial cells mature, they produce hundreds of motile cilia and continue to produce the sonic hedgehog (SHH) ligand, which is found apically in the thin layer of liquid covering airways. However, whether ciliated airway cells express apical HH signaling components and what their function might be have remained unknown. Here we show that motile cilia are enriched for HH signaling proteins, including patched 1 and smoothened. These cilia are also enriched for proteins affecting cAMP-dependent signaling, including Gαi and adenylyl cyclase 5/6. Surprisingly, SHH in differentiated airway epithelia did not elicit the canonical SHH signaling pathway that regulates transcription during development. But instead, activating HH signaling decreases intracellular levels of cAMP, which reduces ciliary beat frequency and airway surface liquid pH, similar to changes that have been observed in the airway of people with chronic obstructive pulmonary disease (COPD). Furthermore, we observed that significant increase of SHH ligand expression in differentiated airway epithelia with COPD, suggesting a potential role of SHH signaling in the pathogenesis of airway disease. Collectively, our study indicates that airway cilia detect apical SHH to mediate airway physiology through noncanonical HH signaling. SHH may dampen defenses at the contact point between the environment and the lung, perhaps counterbalancing processes that stimulate airway defenses. This may suggest a potential role of SHH signaling in the pathogenesis of airway disease, such as COPD.

Pharmaceuticals in the aquatic environment is an emerging issue and the risks they pose are mostly unknown. They are used in large amounts throughout the world and can enter the environment, as the active metabolite or unmetabolised, through excretion by people and improper disposal. As these drugs are designed to have specific biological effects in a specific organism (as well as sometimes having other non-specific side effects), their potential to cause effects within the environment is great. Clofibric acid (the major metabolite of the lipid lowering drug, Clofibrate) is non-biodegradable, highly motile, very persistent and frequently detected at μg/I levels in the environment. I studied possible effects of clofibric acid in fish, using different experimental approaches and endpoints. The studies involve two different species, and for one of these species, fish at different stages of development. The chapters within this thesis have presented the first evidence (albeit preliminary) of clofibric acid having effects on both adult and embryo fish. When fathead minnow embryos were exposed to clofibric acid, the effects seen included changes in the eggshell, time to hatch, hatchability, mortality and viability. Adult fathead minnow were similarly exposed and significant effects on specific parameters were also observed. These included effects on lipid metabolism, steroidogenesis and spermatogenesis - thought to be via cholesterol transport - as well as significant effects on the expression of several genes involved in lipid metabolism and detoxification. Exposure of juvenile (sexually undifferentiated) bream also found significant differences in some endpoints. Other results suggested, less pronounced effects of clofibric acid on some other parameters. The results from this research show that there are effects of clofibric acid in pathways which were not only unexpected in fish (for example, steroidogenesis, spermatogenesis and gene expression), but also at concentrations below those previously shown to have any biological effects on fish. These effects indicate that clofibric acid may potentially have an impact on fish fecundity, and even more worryingly, on human health for those people prescribed it.

No description available.

Advances in time-lapse 3D in vivo fluorescence microscopic imaging techniques enables the observation and investigation into the migration of Oligodendrocyte precursor cells (OPCs) and its role in the central nervous system. However, current practice of image-based OPC motility analysis heavily relies on manual labeling and tracking on 2D max projection of the 3D data, which suffers from massive human labor, subjective biases, weak reproducibility and especially information loss and distortion. Besides, due to the lack of OPC specific genetically encoded indicator, OPCs can only be identified from other oligodendrocyte lineage cells by their observed motion patterns. Automated analytical tools are needed for the identification and tracking of OPCs. In this dissertation work, we proposed an analytical framework, MicTracker (Migrating Cell Tracker), for the integrated task of identifying, segmenting and tracking migrating cells (OPCs) from in vivo time-lapse fluorescence imaging data of high-density cell clusters composed of cells with different modes of motions. As a component of the framework, we presented a novel strategy for cell segmentation with global temporal consistency enforced, tackling the challenges caused by highly clustered cell population and temporally inconsistently blurred boundaries between touching cells. We also designed a data association algorithm to address the violation of usual assumption of small displacements. Recognizing that the violation was in the mixed cell population composed of two cell groups while the assumption held within each group, we proposed to solve the seemingly impossible mission by de-mixing the two groups of cell motion modes without known labels. We demonstrated the effectiveness of MicTracker in solving our problem on in vivo real data. / Doctor of Philosophy / Oligodendrocyte precursor cells (OPCs) are a type of motile cells in the central nervous system (CNS). OPCs' migration plays a critical role in the repair and re-distribution of myelin sheaths, a structures that helps to accelerate the transmission of electrical signals from neuron to neuron. But the mechanism behind the motility of OPCs is largely unclear. In recent years, advances in genetic fluorescence indicators and time-lapse optical microscopic imaging techniques, especially 3D in vivo imaging, enables neuroscientists to investigate into the puzzle. However, current practice of OPC motility analysis heavily relies on compressing the 3D data into 2D then manually tracking the OPCs, which suffers from not only massive human labor, subjective biases, weak reproducibility and especially information loss and distortion. Automated analytical tools are needed. Due to the limitation of current techniques in fluorescent labeling of cells in live animals, OPCs cannot be distinctively labeled. Instead, in the field of view there are also other irrelevant cells that cannot migrate but locally vibrate. Therefore, the human analyzer or the analytical software is supposed to detect OPCs from a cluster of touching cells containing multiple types of cells by their motion patterns only. In this dissertation, we presented a fully automatic machine learning based algorithm, MicTracker (Migrating Cell Tracker), to identify and track migrating OPCs. The task cannot be straightforwardly solved by existing generic-purpose cell tracking tools due to quite a few special challenges. To tackle the challenges, we also proposed novel methods for two major modules of MicTracker, segmentation and linking, respectively. We demonstrated the effectiveness of MicTracker and its components on real data and compared it with related existing works. The results of experiments showed notable superiority of MicTracker in solving our problem, compared with existing methods.

Résumé confidentiel / Confidential abstract

Résumé confidentiel / Confidential abstract

Le cil primaire est une antenne sensorielle présente à la surface de la plupart des cellules qui contrôle des voies de signalisation clés au cours du développement et de l’homéostasie tissulaire. Des défauts de formation ou de fonctionnement des cils sont responsables de maladies génétiques complexes appelées ciliopathies. La néphronophtise (NPH) est une ciliopathie caractérisée par une néphropathie tubulo-interstitielle chronique évoluant généralement vers l’insuffisance rénale terminale (IRT) avant l’âge adulte. La NPH peut être isolée ou associée à des signes extra-rénaux tels que la rétinite pigmentaire et des défauts du squelette permettant de définir des syndromes comme celui de Saldino-Mainzer (MZSDS). La NPH est une maladie à transmission autosomique récessive très hétérogène sur le plan génétique et les protéines codées par les gènes identifiés ont quasiment toutes été impliquées dans des fonctions ciliaires. Le séquençage d’exome de patients, ciblant plus de 1300 gènes ciliaires (ciliome), a permis de mettre en évidence des mutations dans deux nouveaux gènes candidats pour la NPH : CEP83 et TEKT1. Mon travail de thèse a consisté à caractériser l’effet des mutations et à valider leur implication dans les phénotypes des patients. CEP83 a été retrouvé muté chez plusieurs patients non-apparentés présentant une NPH avec IRT précoce (< 5 ans). CEP83 est un composant des appendices distaux du centriole père qui joue un rôle clé dans les étapes précoces de la formation du cil. J’ai montré que les mutations identifiées entraînaient une désorganisation des appendices distaux qui pourrait expliquer les défauts de ciliogénèse observés dans les fibroblastes et les biopsies rénales de patients. Ces résultats ont permis de démontrer l’implication d’une nouvelle protéine centriolaire dans la physiopathologie des formes sévères de NPH. TEKT1 présente des mutations hétérozygotes composites chez un patient ayant un tableau clinique complexe associant un MZSDS et une dyskinésie ciliaire primitive (PCD) due à des défauts de cils motiles. Une analyse génétique détaillée a mis en évidence des mutations sévères dans un second gène, WDR19, déjà caractérisé dans les formes de NPH associées à des défauts osseux. TEKT1 code la protéine Tektine-1, un membre encore non caractérisé de la famille des tektines impliquées dans les cils motiles. L’analyse de cellules nasales multiciliées a montré que Tektine-1 était localisée le long de l’axoneme des cils motiles contrôles et absent des cils des cellules du patient qui présentaient aussi des anomalies sévères de battement. En parallèle, des défauts de ciliogénèse, typiques de mutations de WDR19, ont été observés dans les fibroblastes du patient. Ces résultats suggèrent que ce phénotype complexe est dû aux effets complémentaires des mutations des deux gènes TEKT1 et WDR19, responsables des défauts dans les cils motiles et primaires, respectivement. / The primary cilium is a sensory antenna present on the surface of most of the cells. It controls key signaling pathways during development and tissue homeostasis. Defects in cilia growth or activity are responsible for complex genetic diseases called ciliopathies. Nephronophthisis (NPH) is a ciliopathy characterized by chronic tubulointerstitial nephritis which usually progresses to end-stage renal disease (ESRD) before adulthood. NPH may be isolated or associated with extra-renal defects such as retinitis pigmentosa and skeleton involvement. The combination of these symptoms defines syndromes such as Saldino-Mainzer (MZSDS). NPH is an autosomal recessive disorder highly genetically heterogeneous and almost all of proteins encoded by the identified genes have been involved in ciliary function. The exome sequencing in patients, targeting up to 1300 ciliary genes (ciliome), highlighted new mutations in 2 NPH candidate genes: CEP83 and TEKT1. My work was to characterize the effects of the mutations and validate their involvement in patient phenotypes. CEP83 was found mutated in several unrelated patients with early-onset of NPH (IRT<5 years). CEP83 is a component of distal appendages on the mother centriole which play a crucial role in the early steps of cilia formation. I have shown that the identified mutations perturbed the distal appendages formation which might explain the defects in ciliogenesis observed in fibroblasts and kidney biopsies from patients. These results have demonstrated the involvement of a new centriolar protein in the pathophysiology of NPH severe forms. TEKT1 presents compound heterozygous mutations in a patient with a complex phenotype combining a MZSDS and primary ciliary dyskinesia (PCD) due to defects in motile cilia. The genetic analysis showed mutations in a second gene, WDR19, already characterized in NPH associated with bone defects. TEKT1 encodes the Tektin-1 protein, an uncharacterized member of the tektin family involved in motile cilia. The nasal multiciliated cells analysis showed that Tektin-1 was localized along the axoneme of control motile cilia and absent from the cilia in patient cells, which also had severe beating impairment. In parallel, defects in ciliogenesis, typical of WDR19 mutations, were observed in the fibroblasts from the patient. These results suggest that this dual ciliary phenotype is rather due to the additional effect of mutations in both TEKT1 and WDR19, responsible for the defects in motile and primary cilia, respectively.