OIST Institutional Repository
Not a member yet
2744 research outputs found
Sort by
Anatomical and Functional Study of the Superior Colliculus Pathway to the Inferior Olive in Mice
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe Inferior olive is an important region for motor learning and movement coordination. Its climbing fiber projections to Purkinje neurons drive complex spike activity, a central element in cerebellar function theories. Although the function of the inferior olive has been investigated by the occurrence of complex spikes during motor learning, it remains unclear how its intrinsic properties and activity shape the generation of complex spikes upon receiving sensory stimulation. To investigate how signals from a pre-olivary structure with a well-defined behavioral role affect IO spiking, I focused on an afferent from the midbrain superior colliculus. The superior colliculus is an evolutionarily conserved midbrain region known for its role in mediating orienting-related movements. The SC-IO pathway serves as an excellent model for studying how inferior olive neurons (IO) respond to their inputs. Additionally, this pathway raises the exciting possibility for orienting-related behaviors modulated by learning through the olivo-cerebellar system.
In this study, we explore SC projections to the IO using viral tracers, calcium imaging, and optogenetic stimulation. In addition to the established projections to the medial accessory olive (MAO), we uncover SC axonal projections to the ventral principal olive (PO). Our findings reveal that SC axons terminate on both dendritic shafts and spines of IO neurons, potentially influencing the probability of spike and the network synchronization mediated by gap junctions on dendritic spines.
To demonstrate the ability of SC axons to drive IO spiking, we performed in vivo calcium imaging and showed that optogenetic activation of SC inputs not only induces spiking, but also modulates the overall synchronization of the IO. This study lays a foundational framework for exploring the behavioral relevance of the SC-IO pathway in mice
Development of Red-Emissive Mechanoresponsive Polymers Incorporating Dynamic Photoluminescent Copper(I)-Pyridinophane-Arylamide Mechanophores
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThis thesis describes the preparation, photophysical studies and computational studies of the photoluminescent copper(I)-pyridinophane-arylamide complexes, as well as the mechanoresponsive properties of poly(butyl acrylate) films incorporating these complexes as cross-linkers. First, an introduction will be given on the recent development of mechanoresponsive polymers covalently incorporating organic or organometallic mechanophores. The metal complex-based mechanophore systems will be then introduced, followed by the previous work in our group on the development of copper(I)-iodide and copper(I)-NHC photoluminescent mechanophores bearing a conformationally dynamic N4 pyridinophane macrocyclic ligand.
In the following chapter, novel copper(I)-pyridinophane-arylamide complexes will be introduced. Their preparation, characterization, photophysical properties, electrochemical properties as well as the conformationally fluxional behavior in solution will be discussed, supported by computational studies.
In the final chapter, synthesis and properties of mechanoresponsive polymers incorporating the copper(I)-pyridinophane-arylamide complexes as mechanophores will be presented. Optimization of the preparation method, photophysical properties and the mechanoresponsive properties of these polymers will be discussed
Exploration and Engineering of Protein Sequence Space via Insertions and Deletions
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyProteins are essential molecules for sustaining life and its diversity, mainly composed of 20 amino acids. Despite the vast theoretical possibilities of protein sequence space, nature utilizes only a small, selectively purified area. While previous studies have mainly focused on exploring sequence space with fixed sequence lengths, investigations involving insertions and deletions (InDels) have been limited due to the immense complexity of the sequence space. This thesis addresses this unexplored frontier, providing a systematic exploration and analysis of protein sequence space. The research begins with a comprehensive investigation of the sequence space in the lysozyme-like fold superfamily, establishing a global map of its sequence space in Chapter 1. Chapter 2 focuses on the GH19 chitinase family - an essential enzyme for degradation of fungal pathogen - a selected unexplored region within this space where functional innovations, mediated by InDels, have occurred in remote region of the protein. Chapter 3 extends the findings by exploring strategies to expand and apply these newly explored regions, revealing their broader potential for understanding evolutionary pathways and engineering novel functionalities. Through this work, the thesis deepens our understanding of the dynamics and diversity of protein sequence space, shedding light on evolutionary innovation and providing a foundation for advancing enzyme design and engineering
Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome
Full text linkPlants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae—but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives—especially in defensive, stress-tolerance, and secondary metabolite pathways—yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses
The Topology, Geometry and Physics of Non-Hausdorff Manifolds
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIn this thesis we investigate various mathematical and physical problems surrounding the theory of non-Hausdorff manifolds. We start by introducing a topological theory of nonHausdorff manifolds from first principles. We then pass our discussion into a smooth category by defining various structures of geometric interest on non-Hausdorff manifolds, all whilst circumventing the technical issues surrounding partitions of unity. We complete our mathematical contribution by describing de Rham cohomology for non-Hausdorff manifolds, ultimately proving a generalized version of de Rham’s Theorem. For the physical contribution, we focus our attention on certain two-dimensional non-Hausdorff manifolds that may be interpreted as a type of topology-changing spacetime. We define a gravitational action for 2d non-Hausdorff spacetimes, and determine the angular conventions required to suppress their contribution within a Lorentzian-signature path integral for gravity that sums over topologies
Feedforward Disinhibition of Purkinje Neuron Dendrites by Molecular Layer Interneurons During Sensory/Motor Processing
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyCerebellar Purkinje neurons (PNs) output is critical for motor coordination and cognitive functions. During sensory-motor input, such as air puff stimulation or spontaneous locomotion, PN intrinsic properties and output is modulated by excitatory climbing fiber (CF) and parallel fiber (PF) inputs, and feedforward inhibitory input from 2 types molecular layer interneurons (MLIs), MLI-1 and MLI-2. Traditional models of feedforward inhibition (FFI) assume sustained PF-mediated depolarization of PN dendrites and variable levels of FFI from MLIs. To examine this model, I employed recent advancements in voltage-, Ca2+-, GABA-, and glutamate-imaging. Data revealed that upon spontaneous locomotion onset, glutamatergic input from PFs onto PNs exhibited an initial peak and an elevated glutamate level for approximately 5s, followed by a decrease from baseline. In contrast, GABAergic input from MLIs onto PNs predominantly decreased from the onset of locomotion, suggesting feedforward disinhibition (FFDI) rather than FFI. To study the effect of PN disinhibition, i.e., a decrease in GABA release onto PN dendrites, GABAA and GABAB receptor antagonists were applied in the granule cell layer. Blocking GABA receptors with antagonists resulted in an increase in Ca2+ influx during spontaneous dendritic complex spikes (DCSs). Since GABA does not predominantly suppress PN excitability during sensory-motor input, an alternate possible inhibitory mechanism was investigated. Simultaneous voltage and GABA imaging from PN dendrite also revealed occasional hyperpolarization that was not always correlated with GABA input. To explain the occasional hyperpolarization, the role of small conductance calcium-activated potassium channels (SK2) was investigated. Blocking of SK2, with Apamin, reduced hyperpolarization at PN dendrites following air-puff stimulation. Investigating the mechanisms underlying this GABA input reduction at PNs, imaging MLI-to-MLI GABA inputs indicated a lack of mutual inhibition, suggesting that inter-MLI-inhibition is not responsible for GABA depression at PN dendrites. Additionally, the blockade of endocannabinoid receptors by AM251 did not increase GABA release onto PNs by MLIs, ruling out endocannabinoid involvement. Instead, extracellular electrical stimulation of the molecular layer suggests that GABA depression is driven by vesicle depletion. In summary, this study indicates that contrary to the classical view, MLIs enhance PN excitability through disinhibition, leading to an increase in Ca2+ influx into Purkinje dendrites, while intrinsic KCa channels counteract disinhibition to reduce Purkinje dendrite excitability
Role of Statistics as a Thermodynamic Resource in Quantum Engines
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyUltracold atomic gases serve as ideal platforms for studying complex quantum effects, offering precise control over many degrees of freedom. They are therefore an excellent testbed for exploring fundamental ideas and concepts in quantum thermodynamics, where the principles of quantum mechanics and thermodynamics are linked from first principles. One of the most prominent areas of interest in this field is the study of quantum heat engines—systems in which a quantum working medium undergoes cyclic interactions with hot and cold reservoirs to convert heat into work. In this thesis I explore heat engines that utilize quantum many-body systems as their working medium. At ultracold temperatures, quantum statistical effects play a crucial role, with the fermionic or bosonic nature of the quantum gas directly influencing its energetic behavior. It is therefore an interesting question to ask what an engine that operates based on a quantum statistical energy difference would look like? To address this, I investigate two experimentally realizable settings where quantum statistics can be manipulated: the BEC-BCS crossover in three-dimensional quantum gases and the Lieb-Liniger model in one dimension.
In the first part of this thesis, I introduce the concept of the Pauli engine, a purely quantum engine that operates within the BEC-BCS crossover region. Here, the change in particle statistics effectively replaces conventional heat reservoirs, offering a novel mechanism for work production. I compare the performance of the Pauli engine to both a statistics-based thermal engine and a solely interaction-driven engine. The findings demonstrate that the Pauli engine outperforms both alternatives, establishing quantum statistics as a valuable thermodynamic resource for work extraction. Additionally, I compare my theoretical predictions to experimental data from the realization of the Pauli engine conducted by the group at Kaiserslautern University.
The second part of the thesis focuses on implementing a quantum heat engine using a one-dimensional repulsively interacting Bose gas as the working medium. This system is described by the Lieb-Liniger model, an integrable framework that can be exactly solved using the Bethe ansatz. Within this model, the many-body interactions can be continuously tuned from the non-interacting limit to the strongly interacting Tonks-Girardeau regime, where bosonic atoms exhibit fermionic statistical behavior. Leveraging this statistical transition, I introduce and theoretically analyze two statistically enhanced engine cycles: the A-cycle and the T-cycle. For both cycles, I examine their efficiency at maximum work by optimizing the performance with respect to system length. The results demonstrate that tailoring quantum statistics can significantly enhance engine performance, reinforcing the potential of statistical effects as a thermodynamic resource
Cerebellar Control of Interceptive Motor Behavior in Head-Fixed Mice
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe ability to perform high-precision motor action to intercept a moving object is fundamental to animal motor behavior within a natural environment. Unlike grasping a fixed object, this sensory-motor action requires top-down predictions and bottom-up sensory information to provide online and adaptive movement control.
In the first part of my thesis, I introduce a novel behavioral task where head-fixed mice intercept a moving food pellet with their tongue. I describe the hardware, software, and analysis framework developed for this task and details of the 3D kinematics of discrete tongue-reaching movements, which exhibit distinct motor phases akin to limb reaching. I show how mice learn to coordinate their body movements for successful interception and demonstrate the partial dependence of this behavior on visual inputs.
In the second part of my thesis, I examine the contribution of lateral cerebellar circuits to our interception sensorimotor behavior using pharmacological inactivation and one-photon calcium imaging of Purkinje cell dendrites in Crus I and II. These experiments demonstrate that lateral cerebellar circuits are required for successful performance in the interception task. Moreover, I find that Crus I and II complex spiking activity encodes different aspects of our task. While Crus I primarily encodes sensory-related signals, Crus II encodes motor-related signals. Additionally, both lobules display opposing learning-related dynamics.
Together, the thesis introduces a new behavioral paradigm as a stepping-stone to investigate the neural basis of interception-like behavior in head-fixed mice. I show an interesting division of labor within lateral cerebellar circuits during this dynamic behavior. Moreover, this behavioral paradigm allows for studying discrete, non-rhythmic, precisely timed tongue movements
Catalytic Bond-Formation Reactions at the γ-Position of β-Ketophosphonates: Asymmetric Mannich Reactions and Formal Aldol Condensation Reactions
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOrganocatalytic reactions have been used as an alternative means to enzymatic and organometallic catalysis in accessing functionalized molecules. In this thesis study, organocatalytic regioselective reactions of b-ketophosphonates at the g-position were developed. In the first part, enantioselective g-position-selective Mannich reactions of b ketophosphonates with cyclic sulfonylimines were enabled using 1,3-diamine derivatives and acids as catalysts. 1,3-Diamine derivatives were not previously explored as catalysts, and this study demonstrated the design and use of 1,3-diamine-derived catalysts. In the second part, formal aldol condensation reactions of b-ketophosphonates with arylaldehydes that afford g,d-unsaturated b-ketophosphonates catalyzed by p-anisidine and trifluoroacetic acid were developed. Mechanistic investigations suggest that a Mannich reaction followed by elimination results in the formation of the desired product. Whereas b-ketophosphonates have an active methylene group, in both reactions, g-position-selective C-C bond formations of b-ketophosphonates occurre
Chaos, Correlations and Entanglement in Strongly-correlated 1D Mixtures of Ultra-cold Bosons
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIn this thesis I focus on strongly-correlated multi-species systems of interacting bosons harmonically trapped in one-dimensional space from first principles. More specifically, in the first project, I study the emergence of quantum chaos in a binary mixture of few ultracold bosons in terms of the intra- and inter-species interactions. In particular, I answer an elementary question that is ‘What is the minimum number of interacting particles required to create chaos in a quantum system in the continuum?’. In the second project, I propose a robust scheme for engineering of correlated quantum states as ground states of systems of two distinguishable impurities immersed in a few-boson host medium. Particularly, by scrutinizing the ground-state properties of such system, I demonstrate that the two impurities exhibits non-classical correlations and form Bell states. Importantly, the proposed scheme can be implemented with current ultra-cold atomic settings, where particle numbers and interaction strengths are fully experimentally controllable. In the third project, I employ an ab initio approach to unveil quantum correlations, coherence, and spatial localization in threespecies mixtures of a few repulsively interacting bosons confined harmonically. The goal is to comprehensively explore the ground-state properties and hence illustrate the complete ground-state phase diagram of the three-species correlated system in terms of the intra- and inter-species interactions