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Deciphering the Role of AP-1 Transcription Factor JunB in CD4+ T Cells
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyDifferentiation of distinct CD4+ T effector cell subsets is a key event for adaptive immune responses. Upon recognition of antigens, naïve CD4+ T cells differentiate into functionally distinct CD4+ effector T cell subsets, which control different types of adaptive immunity. The differentiation of CD4+ T effector cells is regulated by the BATF-containing AP-1 heterodimers and their associating proteins IRF4, BATF and IRF4 are induced by T cell receptor (TCR) and co-stimulatory signals and regulate expression of genes required for a broad spectrum of biological functions across diverse CD4+ effector T cell subsets. These transcription factors have been shown to be essential for lineage specification, metabolic activity, and survival of various CD4+ effector T cell subsets, including T helper 1 (Th1), Th2, Th9, Th17, follicular T helper (Tfh) and effector regulator T (eTreg) cells. In contrast to IRF4 and BATF, the role of the major BATF-heterodimeric partner, JunB, in CD4+ T cell differentiation is still not fully understood. In this thesis, I demonstrate that JunB promotes the survival of TCR-stimulated CD4+ T cells under Th1-, Th2-, and Th17-polarizing conditions. Consistent with this, accumulation of antigen-primed JunB-deficient CD4+ T cells are dramatically impaired in mice immunized with complete Freund’s adjuvant (CFA), LPS, or papain. RNA-sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIPseq) analyses reveal that JunB directly regulates expression of various genes that are commonly induced in priming of naïve CD4+ T cells, including a pro-apoptotic gene Bcl2l11 (encoding Bim), and genes that are specifically induced in Th1, Th2, and Th17 cells. Furthermore, JunB colocalizes with BATF and IRF4 at genomic regions for more than 70% of JunB direct responsive genes. Taken together, JunB, in collaboration with BATF and IRF4, serves a critical function in differentiation of diverse CD4+ T cells by controlling common and lineage-specific gene expression
Interaction of multiple inputs in plasticity of the corticostriatal synapses
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyDopamine-dependent plasticity in synapses between the cortical pyramidal neurons and the spiny projection neurons (SPNs) in the striatum is associated with reinforcement learning. Spike timing-dependent plasticity (STDP), which depends on the relative timing of pre- and postsynaptic activity, has been described in these synapses. Previously the STDP profile has been determined by testing single input-output events in isolation from the context of concurrently occurring multiple inputs into the same neuron. However, interactions among synaptic inputs at the level of the dendrites might influence STDP induction. The overall aim of this thesis is to study whether the activation of multiple synaptic inputs alters the characteristics of STDP in the corticostriatal pathway. Whole-cell electrophysiological recordings of SPNs in the dorsomedial striatum (DMS) of mouse brain slices were made in the presence of two inputs stimulated at different time points relative to postsynaptic firing. This protocol induced LTD depending on the timing of each input in SPNs expressing dopamine D1 receptors but not in SPNs expressing D2 receptors. When two inputs showed interactions, indicated by nonlinear summation of evoked EPSPs, STDP profiles were altered from those seen when single inputs were studied. In addition, pairing of two presynaptic inputs without postsynaptic firing also induced LTD, suggesting that pairing of synaptic inputs alone within a temporal window can induce associative synaptic plasticity. In separate experiments, optogenetic release of dopamine two seconds after each pairing modified STDP, depending on the input timing and interactions. Dopamine also modulated associative synaptic plasticity induced in the absence of postsynaptic firing. These results suggest that the rules for synaptic plasticity observed with multiple inputs to the same neuron are not identical to those observed when inputs are tested one at a time per neuron. This new knowledge helps to place STDP in the context of whole brain activity and adds to current understanding of associative learning in the striatum
A Study of Horizontally Transferred Glycosyl Hydrolase Family 6 Genes in Tunicate Genomes
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyTunicates are the closest extant relatives of vertebrates. Tunicates produce cellulosecontaining tunic and exhibit very characteristic lifestyles among animals. Their unique ability to synthesize cellulose results from a horizontally transferred cellulose synthase gene (CesA). Interestingly, a Glycosyl Hydrolase Family 6 (GH6) hydrolase-like domain exists at the C-terminus of tunicate CesA but not in cellulose synthases of other organisms. This led to the identification of another independent GH6-encoding gene, GH6-1, in tunicate genomes. These GH6-encoding genes exist exclusively in tunicates within the animal kingdom. The existence of GH6-encoding genes and the combination of GH6 and cellulose synthase domains raised the question of the evolutionary origin and function of GH6s in tunicates. To answer these questions, I first examined the phylogenetic relationship of GH6- encoding genes by comparing their sequence signatures. Tunicate CesA and GH6-1 genes represent two independent orthologous groups, but the origin of these genes before a horizontal transfer event could not be ascertained. Secondly, I examined the expression of tunicate CesA and GH6-1 genes in Ciona intestinalis type A, a model ascidian tunicate. The gene expression in embryos at early developmental stages was examined by quantitative reverse transcription PCR and in situ hybridization. Obvious expression of both CesA and GH6-1 were found at embryonic stages of Ciona embryo at epidermis. The observed expression profiles were also compared with a set of single-cell transcriptome data provided by our collaborators. Embryonic cells of late tailbud stage I showed that both GH6-1- and CesA-expressing cells are mostly in cell clusters of epidermal identity. Localized signal in the reporter assay also suggest the existence of specific enhancers upstream to Ciona GH6- 1 gene. Finally, I used genome-editing technique to generate GH6-1 knockout larvae of C. intestinalis type A and observed that affected embryos show perturbed papillae formation and metamorphosis. My study showed that GH6-1, a gene very likely originated from horizontal gene transfer, is recruited to function in ascidian early development. This observation would help to address how tunicates evolved by obtaining their unique anatomy and ecology
Topology of Band-Like Excitations in Frustrated Magnets and Their Experimental Signatures
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOne of the most important revolutions in physics during the latter half of the 20thcentury must surely be the introduction of topology. Beginning with the discovery of the integer quantum Hall effect, modern condensed matter theory has now dis-covered a new class of phases with unconventional transport properties. The theory of topologically non-trivial electronic bands in solids is now extremely well-studied. Questions of where similar physics may arise with magnetic excitations have there-fore also gained attention. Magnons and other pseudo-particle spin-excitations forma diverse cast with distinct properties that may be important in quantum metrology or even quantum logic tasks and simulation. In this thesis, we investigate the band-topology of such excitations and their experimental signatures. In our study of the bilayer kagome Heisenberg model we investigate the unconventional excitations of a quantum paramagnet. We show that the Z2 topological invariant known from the time-reversal invariant quantum spin Hall system of electrons makes an appearance here. These are comparable, but not analogous to Krämers pairs in electron transport, and they can be characterized in a similar fashion, but they do not enjoy the same symmetry protection under time-reversal due to their bosonic nature. We describe how bond-nematic terms appear which destroy the Z2 phase. We also study the monolayer spin-polarized kagome Heisenberg model. Our representation theory of the bands allows for the determination of degeneracies as well as interactions which give rise to non-trivial band-gaps. We show how one may associate certain features in the neutron scattering spectra with topological ex-citations. We show that pinch-points and half-moon features found ubiquitously in neutron scattering experiments will undergo characteristic distortions when those bands carry Chern numbers. Our work paves the way for a more systematic experimental characterization and treatment of topologically gapped magnetic excitations and motivates experimental investigation of the spin Nernst effect in for instance quantum dimer mate-rials, or possibly in certain ferro-quadrupolar ordered solids
From Polyps to Colonies: Applying Polyp Bail-Out to Study Coral Coloniality
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyColonial lifestyles have been adopted by the majority of shallow-water stony corals (Cnidaria: Scleractinia), as they facilitate coral responses to environmental changes. Polyp bail-out, a coral stress response featuring colony dissociation and polyp detachment, offers a platform to study coloniality in stony corals. However, employing bailed-out polyps in coral research requires greater understanding of the biology of this stress response. This thesis investigates the molecular basis of polyp bail-out in Pocillopora acuta, a branching coral that is common in the tropical waters of the Indo-Pacific Ocean, and examines bailed-out polyps to study the biological foundation of coral coloniality. First, I probe molecular mechanisms involved in hyperosmosis-induced polyp bail-out, based upon a P. acuta transcriptome assembly. Then, I monitor morphological and genetic changes of bailed-out P. acuta polyps after the induced bail-out response. Finally, I explore transcriptional profiles of bailed-out polyps and those of polyps in normal colonies in order to identify differences between corals at different levels of structural and social complexity. Based on transcriptomic data, activation of tumor necrosis factor and fibroblast growth factor signaling pathways was revealed during initiation of polyp bail-out, possibly linking these pathways to colony dissociation and polyp detachment, respectively. Under ambient conditions, about half of bailed-out polyps displayed morphological recovery and genetic resumption of fundamental cellular processes within five days. Compared with recovered bailed-out polyps, normal colonies showed activation of genes for neurological and circulatory system development. Furthermore, in response to environmental stresses, few genetic changes were shared by bailed-out polyps and colonies, suggesting that coloniality promotes distinctively different stress responses, probably enhancing fitness in stony corals. Interestingly, transcriptomic data also revealed differential expression of angiotensin-converting and endothelin-converting enzymes in the transition between normal colonies and bailed-out polyps. This thesis presents a robust polyp bail-out induction protocol and develops a foundation for its application to coral research. Using this new research model, this thesis presents the first molecular-level study of coral coloniality and identifies genes potentially participating in development of coral colonies, which are expected to be fruitful topics for future studies
The Evolution of Dual Functionality of β-catenin in Metazoans
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe evolution of the multicellular body animals from unicellular organisms is still a significant and long-lasting subject of interest in biology. Acquisition of cell-cell adhesion with cadherin, α- and β-catenin proteins is thought to be tightly coupled with the origin of animal epithelium and consequent evolutionary thrive of animals. On the other hand, much research has shown, in a wide range of animal lineages such as bilaterians and cnidarians, that β-catenin associates with diverse intracellular proteins involved in gene transcription/translation and plays an essential role in the induction of the signalling centre (organiser) during animal embryogenesis. The pleiotropic and evolutionary conserved functions of β-catenin suggest deep evolutionary roots of the β-catenin complexes and involvement in the emergence of basic animal body plan. Recent progress in genomics has identified genes of the cell-cell adhesion complex and signalling machinery of β-catenin in genomes of early-branching animals, including Porifera (sponges) and Ctenophora(comb jellies). However, due to difficulties in applying molecular and genetic technologies in these non-model animals, the ancestral functions of β-catenin complexes remain largely to be explored.In this study, I combined structural, proteomic, and functional approaches to understand evolutionarily conserved features of the β-catenin and its associated proteins. Structural analysis suggests a unicellular origin of the basic architecture of β-catenin protein, while amino acid residues critical in adhesive properties are conserved only within animals. To analyse evolutionarily conserved functional characteristics of basal animal β-catenins, I performed transphyletic studies where the basal animal β-catenins are expressed in Xenopus embryos. A series of proteomics analyses of β-catenin-associated proteins revealed the cadherin catenin complex's deep origin and evolutionary conservation. The transphyletic function studies and detailed sequence analysis also revealed the β-catenin's organiser-inducing function of Cnidaria, Porifera, but not Ctenophora. These data suggest that the primary function of ancestral β-catenin was to play adhesive roles, and its' signalling properties were equipped later during the evolution of basal animals
Worldwide Historical Biogeography of Termites (Blattodea: Isoptera)
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyTermites are of crucial importance in terrestrial tropical and subtropical ecosystems where they play a key role in organic matter decomposition. Termites descent from a wood-feeding cockroach ancestor and diverged from the subsocial wood roach Cryptocercus more than 150 million years ago. Given that the origin of termites predates the breakup of the Pangaea, termites potentially acquired their current distribution pattern by a combination of vicariance, through continental drift, or oceanic dispersal, through over-water rafting or land bridges. The origin of termite distribution, called historical biogeography, can be studied by mean of reconstruction of ancestral distribution on time-calibrated phylogenetic trees. Although several studies have already reconstructed the global historical biogeography of termite lineages within the Neoisoptera, these studies did not investigate non-Neoisoptera termites and overlooked one biogeographic realm with unique fauna, Madagascar. In this project, I used complete mitochondrial genomes to build time-calibrated phylogenetic trees of termites and determine the precise dispersal events of yet unstudied termite lineages to and of yet unstudied biogeographic realms. I sequenced the mitochondrial genomes of about 2500 samples including almost all termite species from North, South, and Central America and representatives of the termite diversity from Madagascar. In the chapters 1 and 2, I resolved the historical biogeography of Rhinotermitinae and the early-branching termite families Hodotermitidae, Stolotermitidae, and Archotermopsidae. In the chapter 3, I resolved the historical biogeography of termites from Madagascar. And in the chapter 4, I produced a near-complete phylogenetic tree of termites from the Americas that I used to study the diversification patterns of termites across the two continents that composed the New World. My thesis sheds light on the historical biogeography of termites at the global scale
Intrinsic Motivation in Creative Activity
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIntrinsic motivation is a fundamental basis for creativity. However, little is known about which factors are essential in a behavioral environment for creative activity. I propose a hypothesis that intrinsic motivation in creative activity is facilitated by a higher variety of expressions using simpler rules. To examine the hypothesis, I conducted a novel human behavioral experiment with 42 participants using the original game designed based on the Game of Life cellular automata. The simplicity of a rule is controlled by the parameters of state transition function and quantified by the complexity measures formulated in the theory of cellular automata. The variety of expression is quantified by the features of the cell states, such as entropy of local patterns and empowerment. The degree of intrinsic motivation is measured by subjective enjoyment, playing time, and frequency of touch interaction. The results of two-way ANOVA of the scores of enjoyment for the four rules showed that participants were more intrinsically motivated with a higher variety of expression and a simpler rule, which supports the hypothesis. Regression analyses revealed that the variety of local patterns was a major factor for subjective enjoyment and also suggested two types of subjects. Subgroup analyses showed that participants had opposite preferences for simple and complex rules. The present results are generally consistent with the hypothesis but point to the necessity of considering individual differences
Investigating Color Centers in Diamond for Microwave Quantum Technologies
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe rapid advancement of quantum technology in recent years has necessitated the development of many specialized microwave components such as the Josephson parametric amplifier (JPA), to be used in conjunction with superconducting qubits. In this thesis, present research into impurity spins in diamond, which include nitrogen (P1), nitrogen vacancy (NV), and vacancy clusters, in particular (R5) centers, for use in these microwave quantum technologies. I first present the development of a 3D loop-gap microwave resonator for use with these impurity spins. We were able to demonstrate strong coupling with an ensemble of nitrogen-vacancy (NV) centers as well as that of nitrogen (P1) centers at 10 mK. I next demonstrate two separate but related maser effects in the spin ensemble. The first of which is a thermally-generated inversion of the NV centers, produced by an abrupt cooling of the sample with a lifetime of several hours. Finally, I demonstrate another spin-based cavity maser, this time using the P1 centers and an active microwave pumping scheme. This cavity amplifier has several desirable qualities, including a large gain and low noise temperature. Such an amplifier may be promising for future quantum technology applications
Atom-Light Interactions via Evanescent Fields
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyRecently developed techniques to operate, control and measure atomic systems on the micro- and nano-meter scale have created a tremendous interest in exploring how the presence of surfaces affects their quantum properties. This is partly driven by the interest to explore further fundamental physics, but on the practical side, atom-chips and other nano-scale devices are poised to become important in our daily lives. In this thesis, I present results obtained by studying how an evanescent field in the vicinity of a dielectric medium affects various quantum systems, namely one and two atom systems, as well as multi-component Bose-Einstein condensates.
An evanescent field corresponds to an exponentially decaying mode above a surface, which emerges due to propagation of an electromagnetic wave inside a confined dielectric medium, such as a flat half-plane, an optical nano-fiber, or a prism. By bringing atoms close to the surface, the coupling to the evanescent field can strengthen the coupling between the atoms, resulting in multiple effects on their properties: frequency shifts can appear, emission rates can be modified and the dipole-dipole interaction between atoms can be enhanced.
In the first project presented in this thesis, I show that the decay rate of two atoms near a flat dielectric surface is different compared to free space and can have oscillatory decaying behavior. This includes directional propagation of information between the atoms with a strength depending on the orientation of the two electric dipole moments, and on the relative location of the atoms to one another and to the surface of the dielectric medium. I also discuss the modification of the spontaneous emission rate when a multi-level atom is placed in the vicinity of an optical nano-fiber. Here the modifications do not only depend on the optical modes of the fiber, but also on the magnetic sub-levels and orientation of the electric dipole moment of the atom.
A very interesting feature of atom-fiber systems is the possibility for spontaneous emission to be chiral. This effect again depends on the form of the available modes of the fiber and the orientation of electric dipole moment of the atom. In a second project I show that chiral emission also leads to a chiral recoil force on the atom and present a closed form expression for it. I then extend my studies to go beyond small systems and consider Bose-Einstein condensates of neutral atoms in the mean field limit. Exposing such systems to evanescent fields can be described as exposure to an artificial gauge field and be used to induce spatially inhomogeneous rotation into the condensate. In this part of the thesis, I show how localised rotation can affect the miscible to immiscible phase transition in two-component systems