Severe malaria caused by Plasmodium falciparum (P. falciparum) remains a leading cause of death in many low and middle income countries. The intraerythrocytic reproduction cycle of the parasite is responsible for all the symptoms and mortality of malaria. The merozoite, first invade a red blood cell (RBC) in the circulation, then grows, develops and multiplies within it by clonal division. Merozoite invasion is a complex process involving dynamic interactions between ligands in the merozoite coat and receptors on the red blood cell membrane. Therefore, filming the complete malaria invasion processes may shed the light on its mechanism. The rationale of this work is that learning how the various ligand-receptor interactions affect invasion phenotypes will lead us to a better understanding of the key biological and biophysical aspects of parasite growth in the blood. The work described has firstly involved the development of an optimised imaging platform for recording egress-invasion sequences. I used live cell microscopy to understand this stage of malarial infection better, by monitoring egress-invasion sequences in live cultures under controlled conditions and addressing the morphology and kinetics of erythrocyte invasion by P. falciparum. In addition, the erythrocyte invasion phenotypes of the various P. falciparum strains were systematically investigated for the first time by live cell microscopy. Furthermore, to better understand genetic recombination affecting erythrocyte invasion phenotypes, progeny from the 7G8 x GB4 cross was compared to their parents. In order to investigate specific receptor-ligand interactions and their distinct functional characterisations at each distinct stage, the enzymes that cleave receptors on the erythrocytes and antibodies targeting ligands on the merozoites were studied and their effects observed using the live-imaging platform. In the results, the functions of ligands on the merozoites demonstrated for the first time distinct and sequential functions of proteins during erythrocyte invasion, which could potentially guide the design of more effective malaria vaccines. In addition, I have designed microfluidic devices for studying blood stage malaria. Polydimethylsiloxane (PDMS) microfluidic devices are optically transparent, non-toxic and have biocompatible features. Building on previous work, I made specific microfluidic devices for achieving a high throughput of egress-invasion observations. Infected red blood cells were delivered into a microfluidic device channel containing cage-like "nests". The nests were designed to selectively trap these stiff, egress-ready cells, in order to obtain streams of merozoites on maturation. Uninfected RBCs were delivered from another input into a long serpentine channel co-flowing with the egressed merozoites. The results indicated that, during P. falciparum erythrocyte invasion under flow conditions, the morphological effect on erythrocytes and the kinetic properties show significant differences to those in static conditions. In addition, with optimised flow rates, it is possible to reach higher throughput of egress-invasion observations than static conditions. Both the static and flow experiments carried out in this study highlight important mechanisms and processes of malaria invasion, and represent new ways of studying blood stage malaria. Precise and high throughout recording of single-event host-pathogen interaction events will allow us to address a new area of fundamental biological questions in future work.

Philosophiae Doctor - PhD / Obesity is a complex metabolic disease of excessive fat accumulation. It is a worldwide epidemic affecting billions of people and its pharmacological management is hampered by drug toxicity and undesirable side effects. Therefore, a need still exists for the development of safe medication for treatment of obesity. Nanotechnology involves the use of small particles at atomic and molecular scale. It has application in medical diagnostics, drug delivery and molecular imaging. Various nanoparticles (NPs) functionalized with different biomolecules have been successfully used in many therapeutic and research applications due to their versatility, ease of chemical synthesis, low toxicity and unique properties. Examples of NPs used in this study are Gold nanoparticles (GNPs) and Quantum dots (QDs). GNPs and QDs are extensively used as drug delivery, labelling and imaging tools in biomedical research. Nanotechnology offers a new potential useful avenue for solving the problem of toxicity of anti-obesity drugs. This could be achieved through targeted drug delivery. In this study, rats were fed a high fed diet (HFD) to induce obesity. The streptavidin conjugated GNPs and QDs were functionalized with biotinylated adipose-homingpeptide (AHP) and/or anti-obesity drug (Gallic acid). Functionalization was characterized using agarose gel electrophoresis, UV-vis spectroscopy and transmission electron microscopy. The binding-specificity and targeting ability of AHP was evaluated in vitro and in vivo. The apoptotic effect of AHP functionalized-drug loaded GNPs (AHP-GA-GNPs) was tested in vitro using APOPercentage TM and Caspase-3 activation assays. The in vitro data indicated that the binding was specific to prohibitin (PHB) expressing cells (MCF-7 and Caco-2), and that the binding was temperature dependent. PHB was confirmed as a target for AHP after overlaying AHP-FITC and anti-prohibitin antibody staining. Cellular uptake was detected on the cells treated with AHP-functionalized NPs as compared to unfunctionalized NPs. The GA and AHP-GA-GNPs reduced cellular viability and induced apoptosis through activation of Caspase-3. The Ex-vivo studies using primary endothelial cells (ECs) isolated from the WAT of lean and obese Wistar rats showed that the binding of AHP was receptor mediated, and specific to receptors differentially expressed in ECs from obese WAT. The in vivo studies showed that, treatment of obese rats with AHP-functionalized NPs resulted in targeted delivery of the NPs to the WAT as compared to those treated with unfunctionalized NPs. Qualitative analysis using fluorescence microscopy and IVIS Luminar XR, live-imaging system showed that the unfunctionalized NPs accumulated mostly in the organs of the reticuloendothelial system, namely: liver, spleen, lungs and kidneys. In contrast, AHP-functionalized NPs accumulated mostly in the WATs as compared to the rest of the organs of the obese rats. Uptake and binding of the NPs to the tissues was quantitatively confirmed by the inductive coupled plasma-optical emission spectroscopy (ICP-OES). In conclusion, this study reports the 1) successful functionalization of GNPs and QDs with AHP, 2) use of AHP-functionalized GNPs and QDs as delivery and imaging agents to the WAT, and 3) potential use of AHP-functionalized drug-loaded GNPs in the treatment of obesity.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22301号 / 医博第4542号 / 新制||医||1040(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 渡邊 直樹, 教授 椛島 健治, 教授 林 康紀 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Glucose homeostasis is fundamental for all living organisms. In vertebrates, the hormone insulin regulates the metabolism of carbohydrates, fats and proteins. In order to sustain the glucose homeostasis, the pancreatic β-cells, which produce and secrete insulin, must coordinate their efforts to secrete the right amounts of insulin required by the organism. In vitro studies, have suggested that a subpopulation of β-cells, referred to as “hub-cells”, coordinate islet Ca2+ dynamics during insulin secretion. However, it is unclear whether the hub-cell model pertains to an in vivo scenario, where the islet is densely vascularized and innervated. In this thesis, we employed the genetically-encoded calcium indicator GCaMP6, confocal imaging and optogenetics, to characterize the Ca2+ dynamics of the zebrafish β-cells in vivo. We found that pancreatic β-cells present endogenous Ca2+ spikes in vivo under basal conditions. These Ca2+ spikes are rapidly suppressed after lowering glucose levels via insulin administration. In addition, the temporal inhibition of blood flow decreases the Ca2+ spikes, suggesting that β-cells are systemically connected. Furthermore, β-cells show a synchronized response to a pericardial glucose injection. Specifically, we found that Ca2+ spikes originate and emanate from a subset of β-cells that are the first to respond to a glucose stimulus. We define these cells as “leader-cells”. We tested if these cells could coordinate the islet in vivo by employing 2-photon laser ablation. Whereas ablation of control cells had no significant effect on the amplitude and duration of the subsequent Ca2+ spikes responses, ablation of leader cells led to a reduction in the Ca2+ response. Furthermore, we developed systems for optogenetic interrogation of β-cells in vivo. We show that the light-gated Cl- ion pump halorhodopsin (NpHR) can be applied to inhibit β-cell depolarization in the zebrafish. We also present the optically orthogonal system of the red Ca2+ indicator K-GECO1 in combination with the blue-shifted channelrhodopsin CheRiff to activate individual β-cell in vivo. Using these new tools, we provide examples where the activation of individual β-cells showed heterogeneous potential to trigger influx of Ca2+ in the rest of the β-cells. Overall, our results led us to propose a hierarchical model of islet coordination. In contrast to the majority of β-cells, which occupy the bottom of the hierarchy since they present low capability to recruit other cells, the leader cells occupy the top levels, being capable to coordinate a majority of the islet’s β-cells.:List of figures xii List of Tables xiii 1. Introduction 1 1.1. Diabetes and insulin 1 1.2. The endocrine pancreas 2 1.3. The diabetes pandemic 4 1.4. β-cell development in zebrafish and mammals 4 1.5. β-cells function and heterogeneity 6 1.6. β-cell coordination 8 1.7. Genetically-encoded calcium indicators 10 1.8. Genetically-encoded optogenetic actuators 13 1.9. Models to study In vivo β-cell coordination 16 2. In vivo β-cell Ca2+ dynamics 19 2.1. β-cells present endogenous Ca2+ spikes in vivo, which are not present ex vivo 19 2.2. Insulin injection reduces endogenous β-cell Ca2+ activity 22 2.3. Pharmacological inhibition of β-cell Ca2+ spikes interferes with glucose control 24 2.4 Transient blood flow interruption decreases β-cell calcium spikes 26 2.5 Glucose bolus leads to a synchronous response of β-cells 29 3. Leader β-cells coordinates Ca2+ dynamics in vivo 32 3.1. High speed 2D and 3D imaging reveals “leader” β-cells 32 3.2. Pan-islet response to glucose is impaired after leader β-cells ablation 41 4. Optically orthogonal toolset for in vivo optogenetics and Ca2+ imaging 46 4.1. Development of optogenetics actuators systems in zebrafish β-cells 46 4.2. Red fluorescent calcium reporters in zebrafish β-cells 47 4.3. In vivo temporal optogenetic silencing of β-cells 50 4.4. In vivo temporal optogenetic silencing of a subset of β-cells can inhibit the islet response 52 4.5. In vivo temporal optogenetic activation of β-cells 55 5. Discussion and future directions 61 5.1. β-cell calcium spikes are systemically influenced 61 5.2. First responder β-cells are present in vivo 64 5.3. Leader β-cells coordinate Ca2+ influx in vivo 66 5.4. β-cell optogenetic interrogation shows heterogeneous potential of individual β-cells for islet coordination 68 6. Materials and methods 75 6.1. Zebrafish strains and husbandry 75 6.2. Transgenic lines generation 76 6.3. Glucose measurements 77 6.4. Pericardial injection of glucose and insulin 77 6.5. Live imaging 77 6.6. Fast whole islet live imaging 78 6.7. Selective two-photon laser ablation of leader cells in the zebrafish islet. 78 6.7. Selective one-photon optogenetic interrogation of β-cells in the zebrafish islet. 79 6.8. Islet blood flow imaging 80 6.9. Mechanical heart stop 80 6.10. Immunostaining 80 6.11. TUNEL assay 81 6.12 Image analysis of GCaMP6s fluorescence intensity from in vivo imaging. 82 6.13 Quantification of GCaMP6s fluorescence intensity 82 6.14 Spatial drift correction images. 83 6.15 Statistical analysis 84 7. References 85 8. Annexes 90 9. Acknowledgments 97 / Die Glukosehomöostase ist für alle lebenden Organismen von grundlegender Bedeutung. Bei Wirbeltieren reguliert das Hormon Insulin den Stoffwechsel von Kohlenhydraten, Fetten und Proteinen. Um die Glukosehomöostase aufrechtzuerhalten, müssen die β-Zellen der Bauchspeicheldrüse, welche Insulin produzieren und absondern, ihre Bemühungen koordinieren, um die richtigen Mengen an Insulin zu sekretieren, die der Organismus benötigt. In-vitro-Studien haben gezeigt, dass eine Subpopulation von β-Zellen, die als „Hub-Zellen“ bezeichnet werden, die Insulinsekretion der Inseln koordiniert. Es ist jedoch unklar, ob sich die Hub-Cell-Theorie auf ein in-vivo-Szenario bezieht, bei dem die Insel dicht vaskularisiert und von Neuronen innerviert ist. In dieser Arbeit verwendeten wir den genetisch kodierten Calcium-Indikator GCaMP6, konfokale Bildgebung und Optogenetik, um die Ca2+-Dynamik der Zebrafisch-β-Zellen in vivo zu charakterisieren. Wir fanden heraus, dass Pankreas-β-Zellen in vivo unter basalen Bedingungen endogene Ca2+-Spitzen aufweisen. Diese Ca2+-Spitzen werden nach Senkung des Glukosespiegels durch Insulinverabreichung schnell unterdrückt. Darüber hinaus verringert die zeitliche Hemmung des Blutflusses die Ca2+-Spitzen, was darauf hindeutet, dass β-Zellen systemisch verbunden sind. Darüber hinaus zeigen β-Zellen eine synchronisierte Reaktion auf die perdikale Glukoseinjektion. Insbesondere fanden wir heraus, dass Ca2+-Spitzen von den β-Zellen hervorgerufen werden, die zuerst auf den Glukosestimulus reagieren. Wir definieren diese Zellen als 'Leader-Zellen'. Wir haben in vivo durch den Einsatz einer 2-Photonen-Laserablation getestet, ob diese Zellen die Insel koordinieren können. Während die Ablation von Kontrollzellen keinen signifikanten Einfluss auf die Amplitude und Dauer der nachfolgenden Ca2+-Spitzenreaktionen hatte, führte die Ablation von Leader-Zellen zu einer signifikanten Verringerung der GCaMP-Reaktion. Darüber hinaus haben wir Systeme für die optogenetische Abfrage von β-Zellen in vivo entwickelt: Wir zeigen, dass die lichtgesteuerte Cl—Ionenpumpe Halorhodopsin (NpHR) angewendet werden kann, um die Depolarisation von β-Zellen in vivo zu hemmen. Wir präsentieren auch das optisch orthogonale System des roten Ca2+-Indikators K-GECO1 in Kombination mit dem blauverschobenen Channelrhodopsin CheRiff, um einzelne β-Zellen in vivo abzufragen. Unter Verwendung dieser neuen Werkzeuge liefern wir Beispiele, bei denen die Aktivierung einzelner β-Zellen ein heterogenes Potenzial für die Auslösung des Ca2+-Einstroms in die übrigen β-Zellen in vivo zeigte. Insgesamt bietet diese Studie Hinweise darauf, dass eine Untergruppe von β-Zellen ein hohes Potenzial zur Koordination der Ca2+-Dynamik der Insel in vivo aufweist.:List of figures xii List of Tables xiii 1. Introduction 1 1.1. Diabetes and insulin 1 1.2. The endocrine pancreas 2 1.3. The diabetes pandemic 4 1.4. β-cell development in zebrafish and mammals 4 1.5. β-cells function and heterogeneity 6 1.6. β-cell coordination 8 1.7. Genetically-encoded calcium indicators 10 1.8. Genetically-encoded optogenetic actuators 13 1.9. Models to study In vivo β-cell coordination 16 2. In vivo β-cell Ca2+ dynamics 19 2.1. β-cells present endogenous Ca2+ spikes in vivo, which are not present ex vivo 19 2.2. Insulin injection reduces endogenous β-cell Ca2+ activity 22 2.3. Pharmacological inhibition of β-cell Ca2+ spikes interferes with glucose control 24 2.4 Transient blood flow interruption decreases β-cell calcium spikes 26 2.5 Glucose bolus leads to a synchronous response of β-cells 29 3. Leader β-cells coordinates Ca2+ dynamics in vivo 32 3.1. High speed 2D and 3D imaging reveals “leader” β-cells 32 3.2. Pan-islet response to glucose is impaired after leader β-cells ablation 41 4. Optically orthogonal toolset for in vivo optogenetics and Ca2+ imaging 46 4.1. Development of optogenetics actuators systems in zebrafish β-cells 46 4.2. Red fluorescent calcium reporters in zebrafish β-cells 47 4.3. In vivo temporal optogenetic silencing of β-cells 50 4.4. In vivo temporal optogenetic silencing of a subset of β-cells can inhibit the islet response 52 4.5. In vivo temporal optogenetic activation of β-cells 55 5. Discussion and future directions 61 5.1. β-cell calcium spikes are systemically influenced 61 5.2. First responder β-cells are present in vivo 64 5.3. Leader β-cells coordinate Ca2+ influx in vivo 66 5.4. β-cell optogenetic interrogation shows heterogeneous potential of individual β-cells for islet coordination 68 6. Materials and methods 75 6.1. Zebrafish strains and husbandry 75 6.2. Transgenic lines generation 76 6.3. Glucose measurements 77 6.4. Pericardial injection of glucose and insulin 77 6.5. Live imaging 77 6.6. Fast whole islet live imaging 78 6.7. Selective two-photon laser ablation of leader cells in the zebrafish islet. 78 6.7. Selective one-photon optogenetic interrogation of β-cells in the zebrafish islet. 79 6.8. Islet blood flow imaging 80 6.9. Mechanical heart stop 80 6.10. Immunostaining 80 6.11. TUNEL assay 81 6.12 Image analysis of GCaMP6s fluorescence intensity from in vivo imaging. 82 6.13 Quantification of GCaMP6s fluorescence intensity 82 6.14 Spatial drift correction images. 83 6.15 Statistical analysis 84 7. References 85 8. Annexes 90 9. Acknowledgments 97

A feature of prion disease and other protein misfolding neurodegenerative disease is the formation of amyloid plaques. Amyloid is commonly found in the brain of individuals who have died from prion disease and Alzheimer’s disease. The formation and purpose of amyloid in such diseases is poorly understood and it is not currently known whether the material is neurotoxic, neuroprotective or an artefact. Several methods are used to investigate the formation of amyloid both in vitro and in vivo. A cell free protein conversion assay has been optimised to gain insight into the protein misfolding pathway and prion infection has been introduced to a newly characterised whole brain organotypic slice culture model. Fibrillar, but not oligomeric, recombinant PrP species induce a seeding effect on amyloid formation in the protein conversion assay. Brain homogenate containing amyloid from a β-amyloid aggregation mouse model is demonstrated to have a similar effect to recombinant fibril seeds with a PrP substrate indicating a cross-seeding effect. A whole brain organotypic slice culture (BOSC) model has been developed and slices maintained in culture for up to 8 months. During this time slices remain viable with low levels of stress and thin down from 400μm to 30-50μm with morphological consequences. A prominent glial scar forms on the surface of the slice as a result of astrocyte activation and proliferation. The neuronal population decreases while the microglia have a consistent presence throughout time in culture. Replication of misfolded prion protein has been successfully demonstrated within whole BOSC following prion infection after 2 months in culture. The BOSC model represents an accessible short term in vitro model of the brain which can offer insights into protein misfolding in a complex multicellular context. Amyloid formation has been investigated in vivo using a β-amyloid misfolding mouse model following seeding with a range of recombinant protein and brain homogenate seeds. No seeding effect was observed in animals which had received intracerebral inoculations compared to control animals within the time frame of the experiment. A lack of overall amyloid within all animals at the final time point investigated suggests later time points are required for observation of seeding. The functional role of amyloid in protein misfolding neurodegenerative diseases remains unclear. From the cell free protein conversion assay oligomers do not form on the direct pathway towards amyloid in prion misfolding. BOSC provide an accessible and useful short term in vitro model which retains multiple characteristics of the brain. BOSC support replication of misfolded protein and amyloid formation therefore this model can now be utilised to investigate plaque growth and the effect of amyloid formation on surrounding cells. Results from these assays provide important information to guide future in vivo studies and aid the search for therapeutic intervention in these devastating diseases.

Les gamètes femelles appelés ovocytes sont produits par un type spécifique de division cellulaire appelée méiose. Afin de produire des gamètes haploïdes, et contrairement aux divisions mitotiques des cellules somatiques, la méiose implique une seule étape de réplication du génome suivie de deux étapes de ségrégation des chromosomes. La fidélité de la ségrégation des chromosomes pendant la méiose est cruciale pour éviter l’aneuploïdie embryonnaire qui entraînerait des défauts de développement ou un avortement spontané. Dans la plupart des types cellulaires, la ségrégation des chromosomes repose sur un fuseau composé de microtubules. En parallèle à l'assemblage du fuseau, des complexes multi-protéiques appelés kinétochores s’assemblent sur le côté des chromosomes et leur permettent d’interagir avec les microtubules dynamiques du fuseau. Étonnamment, la ségrégation des chromosomes dans l'ovocyte de C. elegans se déroule d'une manière atypique indépendante des kinétochores. Le mécanisme alternatif utilisé dans ces oocytes pour la ségrégation des chromosomes est cependant inconnu. Au cours de mon doctorat, j'ai utilisé une combinaison d'imagerie photonique à haute résolution temporelle, corrélée à de la microscopie électronique à haute résolution spatiale. J’ai également utilisé de la photoablation par laser des microtubules et réalisé l'inhibition ciblée de protéines clés pour disséquer le mécanisme atypique de ségrégation des chromosomes dans l'ovocyte de C. elegans. Mes résultats montrent que la ségrégation des chromosomes est produite par une force dépendante des microtubules qui pousse les chromosomes. Par une analyse détaillée de l’organisation des microtubules dans des fuseaux en anaphase partiellement reconstruits par microscopie électronique en tomographie, je propose un modèle impliquant la génération de force par l'allongement d’un réseau de courts microtubules formant le fuseau central. De plus, je démontre que l'activité de l'orthologue de CLASP chez C. elegans (CLS-2) est essentielle pour l'assemblage du fuseau en anaphase. Ce travail est actuellement sous presse dans le journal Nature Communications. Parallèlement, j'ai disséqué le rôle de CLS-2 dans l'assemblage du fuseau d'ovocytes et la ségrégation chromosomique. J'ai perturbé de manière systématique les domaines individuels et les résidus conservés de manière évolutive dans CLS-2 pour déterminer leur contribution à la fonction et à la localisation de cette protéine pendant la première méiose femelle. Dans l'ensemble, mes résultats montrent que la ségrégation chromosomique dans l'ovocyte de C. elegans consiste en un mécanisme de poussée chromosomique atypique et dépendant de CLS-2. / Female gametes called oocytes are produced through a specific type of celldivision termed meiosis. In order to produce haploid gametes, and unlike mitoticdivisions of somatic cells, meiosis involves a single round of genome replication followed by two rounds of chromosome segregation. Accuracy of chromosome segregation during meiosis is crucial to avoiding embryonic aneuploidy that wouldlead to developmental defects or spontaneous abortion. In most cell types,chromosome segregation relies on a microtubule-based spindle. Concomitant tospindle assembly, multi-protein complexes termed kinetochores assemble on the side of chromosomes and couple microtubule dynamics to chromosomal movements. Strikingly, in the C. elegans oocyte chromosome segregation occurs in an atypical kinetochore-independent manner. The alternative mechanism used in these oocytes for chromosome segregation is however unknown. During my PhD, I used a combination of high spatial and temporal resolution live imaging, correlated light and electron tomography, laser-mediated photoablation of microtubules, and targeted inhibition of key proteins to dissect this a typical mechanism of chromosome segregation in the C. elegans oocyte. Myresults show that chromosome segregation is driven by a microtubule-dependent force that pushes the segregating chromosomes apart during anaphase. Aftercareful analysis of partially reconstructed anaphase spindles by electrontomography for microtubule quantity, length, orientation, and overlaps, I proposea model involving the elongation and/or sliding of tiled microtubules in the central spindle as the candidate structure responsible for this force generation. Additionally, I demonstrate that the activity of the C. elegans CLASP ortholog CLS-2 is essential for proper anaphase spindle assembly. This work is currently in press at Nature Communications.In parallel, I have more closely examined the role of the C. elegans CLS-2 in oocyte spindle assembly and chromosome segregation. I have thoroughly and systematically perturbed the individual domains and evolutionarily conserved residues in CLS-2 to determine their contribution to the function and localization ofthis protein during the first female meiosis. Overall my results show that chromosome segregation in the C. elegans

During vertebrate embryo development, the body axis is subdivided into repeated structures, called somites. Somites bud off from an un-segmented tissue called the pre-somitic mesoderm (PSM) in a sequential and periodic manner, tightly controlled by an in built molecular clock, called the "segmentation clock". According to current understanding, the clock is comprised of: (i) an autonomous cellular oscillator consisting of an intracellular negative feedback loop of Her genes within the PSM cells, (ii) Delta-ligand and Notch-receptor coupling that facilitates synchronization of oscillators among the PSM cells, (iii) Tissue level waves of gene expression that emerge in the posterior PSM and move coherently towards anterior, leading to global arrest of oscillations in the form of somites. However, the movement of cellular oscillators within the PSM before the formation of somitic furrows, a prominent feature of the tissue as observed through this work has not been experimentally considered as a constituent of the segmentation clock so far. Our work aims to incorporate movement of cellular oscillators in the framework of the segmentation clock. It is well known from theoretical studies that the characteristics of relative motion of oscillators affect their synchronization properties and the patterns of oscillations they form. Particularly, theoretical studies by Uriu et al., PNAS (2010) suggest that cell movements promotes synchronization of genetic oscillations. Here, we established experimental techniques and image analysis tools to attain quantitative insight on (i) diffusion co-efficient of cellular oscillators, (ii) dynamics of a population of oscillators, within the PSM aiming towards concomitant understanding of the relationship between movement and synchronization of cellular oscillators. In order to quantitatively relate cellular oscillators and their motion within the PSM, I established imaging techniques that enabled visualization of fluorescenctly labeled nuclei as readouts of cell positions in live embryo, and developed dedicated segmentation algorithm and implemented tracking protocol to obtain nuclei positions over time in 3D space. Furthermore, I provide benchmarking techniques in the form of artificial data that validate segmentation algorithm efficacy and, for the first time proposed the use of transgenic embryo chimeras to validate segmentation algorithm performance within the context of in vivo live imaging of embryonic tissues. Preliminary analysis of our data suggests that there is relatively high cell mixing in the posterior PSM, within the same spatial zone where synchronous oscillations emerge at maximum speed. Also, there are indications of gradient of cell mixing along the anterior-posterior axis of the embryo. By sampling single cell tracks with the help of nuclei markers, we have also been able to follow in vivo protein oscillations at single cell resolution that would allow quantitative characterization of coherence among a population of cellular oscillators over time. Our image analysis work flow allows testing of mutant embryos and perturbation of synchrony dynamics to understand the cause-effect relationship between movement and synchronization properties at cellular resolution. Essentially, through this work, we hope to bridge the time scales of events and cellular level dynamics that leads to highly coordinated tissue level patterns and thereby further our understanding of the segmentation clock mechanism.

京都大学 / 新制・論文博士 / 博士(医学) / 乙第13427号 / 論医博第2231号 / 新制||医||1053(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 松田 道行, 教授 渡邊 直樹, 教授 川口 義弥 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

During vertebrate embryo development, the body axis is subdivided into repeated structures, called somites. Somites bud off from an un-segmented tissue called the pre-somitic mesoderm (PSM) in a sequential and periodic manner, tightly controlled by an in built molecular clock, called the "segmentation clock". According to current understanding, the clock is comprised of: (i) an autonomous cellular oscillator consisting of an intracellular negative feedback loop of Her genes within the PSM cells, (ii) Delta-ligand and Notch-receptor coupling that facilitates synchronization of oscillators among the PSM cells, (iii) Tissue level waves of gene expression that emerge in the posterior PSM and move coherently towards anterior, leading to global arrest of oscillations in the form of somites. However, the movement of cellular oscillators within the PSM before the formation of somitic furrows, a prominent feature of the tissue as observed through this work has not been experimentally considered as a constituent of the segmentation clock so far. Our work aims to incorporate movement of cellular oscillators in the framework of the segmentation clock. It is well known from theoretical studies that the characteristics of relative motion of oscillators affect their synchronization properties and the patterns of oscillations they form. Particularly, theoretical studies by Uriu et al., PNAS (2010) suggest that cell movements promotes synchronization of genetic oscillations. Here, we established experimental techniques and image analysis tools to attain quantitative insight on (i) diffusion co-efficient of cellular oscillators, (ii) dynamics of a population of oscillators, within the PSM aiming towards concomitant understanding of the relationship between movement and synchronization of cellular oscillators. In order to quantitatively relate cellular oscillators and their motion within the PSM, I established imaging techniques that enabled visualization of fluorescenctly labeled nuclei as readouts of cell positions in live embryo, and developed dedicated segmentation algorithm and implemented tracking protocol to obtain nuclei positions over time in 3D space. Furthermore, I provide benchmarking techniques in the form of artificial data that validate segmentation algorithm efficacy and, for the first time proposed the use of transgenic embryo chimeras to validate segmentation algorithm performance within the context of in vivo live imaging of embryonic tissues. Preliminary analysis of our data suggests that there is relatively high cell mixing in the posterior PSM, within the same spatial zone where synchronous oscillations emerge at maximum speed. Also, there are indications of gradient of cell mixing along the anterior-posterior axis of the embryo. By sampling single cell tracks with the help of nuclei markers, we have also been able to follow in vivo protein oscillations at single cell resolution that would allow quantitative characterization of coherence among a population of cellular oscillators over time. Our image analysis work flow allows testing of mutant embryos and perturbation of synchrony dynamics to understand the cause-effect relationship between movement and synchronization properties at cellular resolution. Essentially, through this work, we hope to bridge the time scales of events and cellular level dynamics that leads to highly coordinated tissue level patterns and thereby further our understanding of the segmentation clock mechanism.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21341号 / 医博第4399号 / 新制||医||1031(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 小川 誠司, 教授 坂井 義治, 教授 武藤 学 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM