OIST Institutional Repository
Not a member yet
2744 research outputs found
Sort by
Role of Island Systems in Mangrove Biogeography
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIsland mangrove populations are connected by hydrochory (dispersal via water) in space and time. Yet connectivity studies focusing on island mangroves are still scarce compared to those addressing continental mangroves. There are two distinct mangrove biogeographic regions, the Indo-West Pacific (IWP) and the Atlantic-East Pacific (AEP). In the IWP, both taxonomic and degradation hotspots are located in archipelagos, and more than half of mangrove habitat occurs on islands. As habitat loss and fragmentation continue, understanding of recruitment and population connectivity of island mangroves is critical for mangrove conservation. Moreover, long-distance dispersal and local retention of mangrove propagules depend on species dispersal abilities and land/seascape characteristics. However, demographic rates and historical population changes of island mangrove systems are still largely unknown, especially at a local scale. Thus, this thesis examined island mangrove connectivity in the IWP and focused on one archipelago as a model site to quantify local-scale measures of mangrove connectivity. First, I investigated biogeographic roles of island mangroves in regional mangrove distribution. Using the graph-theoretical method on presence-absence data, I reconstructed the biogeographic structure of the IWP and identified biogeographic roles of species and mangrove sites, which provided insights into how distant mangrove islands are connected, e.g., transoceanic dispersal or stepping-stones. Outputs were then qualitatively compared with paleogeographic studies, population genetic studies, and oceanographic studies to explore which characteristics affect island biogeographic structure and roles. The results showed 4 biogeographic modules (areas with similar floral composition) in the IWP. The distribution of each module was influenced differently by geological events and dispersal parameters, depending on their locations. Furthermore, site biogeographical roles showed intricate networks of stepping stones that constructed ambiguous modules in the region. Individual islands showed heterogeneous species compositions, even within modules, and no area appeared to serve as a biogeographic hub in the IWP. Secondly, I sought to identify localscale population connectivity, focusing on detecting the spatiotemporal scale of propagule dispersal using a multi-disciplinary approach, including population genetic and oceanographic methods. The model site included four islands of the Ryukyu Archipelago in southwestern Japan. Population genetic analyses based on microsatellite markers detected a few contemporary migrations among islands, with overall infrequent genetic exchange among and within islands. In-situ release-recapture experiments employing GPS drifters produced a subset of successful beaching probabilities and supported genetic results that population connectivity was too stochastic and rare to homogenize the genetic structure in the archipelago. To conclude, islands serve as stepping-stones, facilitating species exchange across the IWP. This may create regional biogeography resilient to habitat loss, but also suggests the potential for site losses to become critical gaps that restrict connectivity. Networks of stepping stones are complex and depend on local population connectivity that determines the role of island groups as meta-communities. Moreover, despite competent dispersal abilities, the spatiotemporal scale of mangrove dispersal among islands must be locally quantified using a multi-disciplinary approach. The results from all methods, scales, and resolutions tested in this study to evaluate island mangrove population connectivity suggest that dispersal is primarily localized, and that rare, inter-island dispersal events may maintain regional connectivity
Single Cell Transcriptome Analysis Reveals Heterogeneity and a Dynamic Regenerative Response of Quiescent Radial Glia in Zebrafish Adult Brain
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyNeural regeneration in response to brain damage is an essential topic in medical science. In general, humans have a low regenerative capability. In contrast, zebrafish show a remarkable ability to regenerate neural tissue in response to various types of brain injury. Radial glial cells (RG) that comprise the adult neural stem cell (aNSC) population in zebrafish telencephalon produce non-glial- neural precursor cells that potentially replace the lost neuronal population. However, there is little characterization on how diverse subpopulations of RG respond to the brain injury. We applied single-cell transcriptomics to RG in zebrafish adult telencephalon and identified five RG subtypes, comprising a four quiescent RG (qRG) and one proliferating RG (pRG). One qRG subtype showed a high expression of ribosomal proteins, and its fraction is increased in response to brain damage. Consistently, the mTOR pathway was activated in RG near the injury site. It was reported that inflammatory response of brain-resident immune cells, microglia, is required for inducing regenerative response of RG in zebrafish. Genetical elimination of microglia not only suppressed damage-induced regenerative response of RG but also decreased fraction of the ribosomal expression-enriched RG. Lastly, our pseudo-time analysis revealed a lineage to generate the ribosomal expression-enriched RG. Our analysis revealed heterogeneity of qRG in zebrafish adult brain and their dynamic regenerative response to brain damage
High-Throughput Screening of Cell-Free Riboswitches for Chemical Communication between Microdroplets
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyRiboswitches have recently attracted the attention of synthetic biologists as an alternative to transcription factors for genetic regulation because of their engineerability, relative simplicity, and potential for responding to a wide array of chemical signals. However, biological constraints such as cell permeability, metabolic stability, and toxicity of their chemical ligands have prevented the development of some of those devices using conventional approaches with living cells. Cell-free systems are generally not subject to such constraints and offer a unique platform for building biochemical and genetic systems that display complex functions without using living cells. Efforts to engineer regulatory components directly in cell-free systems thus far have been based on low-throughput experimental approaches, limiting the availability of basic components for building genetically programmed cell-free systems. Here, I report a high-throughput screening method for engineering riboswitches directly in a cell-free system. Fluorescence-activated droplet-sorting (FADS) of randomized riboswitch libraries in a cell-free protein synthesis (CFPS) system rapidly identified cell-free riboswitches that respond to histamine and ciprofloxacin, compounds that are normally not compatible with conventional bacterial screening methods. Finally, the riboswitches obtained through this method were used to demonstrate chemical communication between microdroplets in a self-contained system
SynGAP Condensates Recruit PSD95, and Selectively Retain Multivalent Receptors, Functioning as the Basic Platform for Generating Neuronal Excitatory Synapses
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe post-synaptic structure consists of nano-scale domains that need to be precisely apposed to pre-synaptic neurotransmitter release sites. This exquisite assembly of post-synaptic receptors and scaffold proteins is essential for proper synaptic function. However, the biophysical mechanisms that retain receptors and scaffold proteins at the post-synapse are not well understood. Specifically, a mechanism that can induce clusters of PSD95, a key scaffold protein, at low concentrations, such as those expected before the formation of functional post-synapses, and which can induce long-term retention of post-synaptic receptors, remains to be postulated. In this thesis, I show that SynGAP forms phase-separated condensates through homophilic interactions mediated by its C-terminal coiled-coil domain as well as its intrinsically disordered region. SynGAP recruits PSD95 into these condensates, and this allows recruitment and immobilization of receptors such as Neuroligin and AMPA receptors (via TARPs), which have PDZ binding sites. I also found that oligomerization of Neuroligin and AMPA receptors anchors these receptors in SynGAP condensates. Functional oligomeric Neuroligin and AMPA receptors (GluA1 subunits linked to TARP ษค2) are immobilized for longer durations as they diffuse through phase-separated condensates containing PSD95, compared to monomeric Neuroligin and TARP ษค2. Together, these discoveries reveal how liquid-like assemblies of SynGAP can recruit PSD95 molecules, and retain trans-membrane receptors like Neuroligin and AMPA receptors depending on their oligomerization state
Cross-genome Comparison of Global Oikopleura dioica Populations
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyLarvaceans represent the second most abundant zooplankton in all the worldโs oceans, with key roles in marine food chains and global carbon flux. Oikopleura dioica is a free-swimming planktonic tunicate from the group and possesses the smallest animal genome with extremely dynamic organization: multiple genomic features such as transposon diversity, intron repertoire, gene content and order are altered in Oikopleura compared with other metazoans. Intriguingly, such genome reorganization has not affected the preservation of their ancestral morphology, since O. dioica maintains a chordate-like body plan throughout its life. O. dioica can be easily distinguished from other larvaceans mainly based on separate sexes and the presence of two subchordal cells on its tail. My research is focused on the cross-genome comparison of three O. dioica populations sampled from the Northern hemisphere: one from North Atlantic (Barcelona/Bergen) and two from Pacific (Osaka/Aomori and Okinawa/Kume) Oceans. For each population, I generated high-quality genome assemblies using a combination of short- and long-read sequencing technologies, as well as chromatin conformation data, confirming preservation of three chromosome pairs. A pairwise comparison of populations revealed a striking degree of genome reshuffling that involves a vast number of synteny breaks and rearrangements. My research also shows that rearrangements mostly happen within individual chromosomes and generally preserve protein-coding features, such as genes and their constituent exons, although the gene order has been effectively randomized. O. dioica populations exhibit differences in repeats and gene content that affect even evolutionary conserved clusters, such as Hox genes. Consistent with an increased evolutionary rate, the accumulation of rearrangements in O. dioica appears to have happened much faster than in other animals and resulted in the divergence of multiple lineages of dioecious Oikopleura. The fact that their morphology stayed virtually identical makes O. dioica a perfect model to study genotype-phenotype correlation and the possible existence of unknown regulatory mechanisms.
Overall, my thesis contributes new insights into the evolution of chordate genomes and, thus, may be interesting beyond the field of Oikopleura research
Evanescent Field Mediated Interactions of Cold Rubidium Atoms with Optical Nanofiber Guided Light
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOptical nanofibers (ONFs) have shown promising potential for quantum technology developments. The tight transverse confinement of guided light over an extended length (> 1000!) offers strong atom-light interactions with potential long-range atom-atom interactions mediated by the guided light, allowing for better scalability in many quantum information applications than their corresponding free-space implementations. We demonstrated, experimentally, an electric quadrupole transition and a single-frequency two-photon transition in cold 87Rb atoms driven by nanofiber-guided light, establishing ONFs as excellent platforms for potential applications in compact fiber-based clocks and correlated photon pair sources. ONFs are well-suited for nonlinear collective interactions, such as four-wave mixing and superradiance, that require an ensemble of phase-matched quantum emitters coupled to a common radiation field. An effective system is a 1D array of few hundred atoms trapped near an ONF surface and coupled with the guided mode. A crucial requirement is maximizing the number of trapped atoms which remains challenging in the absence of a quantitative description of atom dynamics during the trap-loading process involving many-body interactions and complex scattering process. We experimentally optimized, leveraging the ability of machine learning algorithms, the number of 87Rb atoms loaded in a shallow fiber-based dipole trap by parametrizing the control of magneto-optical trap parameters. This sets the first step toward planned studies on optical nanofiber mediated collective atom-light interactions and nearest-neighbor interactions in a 1D lattice of Rydberg atoms
Mathematical Modeling and Numerical Analysis of Unstretchable Elastic Ribbons
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyBeing able to model stable states of elastic ribbons can be beneficial for understanding various natural phenomena in physics, biology and chemistry. Ribbons also find their application in engineering. However, identifying stable state of an unstretchable elastic ribbon is a hard task. When modeling a material that bends easily but cannot extend or contract much without tearing or creasing as a two-dimensional elastic body, its resistance to elongation and contraction can be incorporated considering only deformations under which the distances between material points are preserved. The primary objective of this thesis is to develop numerical methods for finding stable equilibria of an unstretchable two-dimensional elastic material bent so that its short edges are joined, with or without twist, to form a closed band. For certain parametrizations of the reference and deformed surfaces, a dimension reduction converts the problem to one involving a system of ordinary differential equations for a pair of vector fields satisfying certain constraints that derive from the requirement that the material be unstretchable and periodicity or antiperiodicity conditions that incorporate the way in which the short edges of the strip are joined. We discretize this problem to obtain a multi-dimensional constrained optimization problem that is solved numerically. To incorporate the discrete isometry constraints, we use Lagrange multipliers approach and minimize an accordingly augmented version of the bending energy. Additionally, we introduce an alternative constraint to ensure that the deformation is injective. The new constraint is bilateral and obviates the need to impose inequality constraints, removes a certain singular feature of the energy density and circumvents symmetry assumptions that have been imposed in all previous studies of this kind
Characterization of Nanoscale Defects in Hybrid Perovskite Thin Films for Photovoltaic Applications
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyHybrid halide perovskites have emerged as one of the most promising contenders for next generation, low-cost photovoltaic technologies. Thanks to the remarkable optoelectronic properties of hybrid perovskite absorbers, perovskite solar cells now achieve efficiencies comparable to conventional inorganic solar cells (Si, GaAs), despite being actively researched for only about a decade. The ability to be processed from solution and to be deposited on transparent and flexible substrates, makes them very attractive for various photovoltaic applications. However, before their wide commercialization, hybrid perovskites need to overcome important limitations. In particular, the presence of defects in perovskite thin films has been detrimental to material properties, and has been a critical reason preventing devices from reaching their full potential. To successfully deploy hybrid perovskites, we must understand the nature of the different types of defects, assess their potentially varied roles in device performance, and understand how they respond to passivation strategies. In this thesis, we employed photoemission electron microscopy to directly image nanoscale defects, and uncovered the presence of multiple types of defects in state-of-the-art perovskite thin films. By adding time resolution to our photoemission electron microscopy measurements, we found that depending on their nature, these defects played varied roles in charge carrier trapping โ from highly detrimental to relatively benign. Further, we also found them to show varied response to passivation strategies, as seen from our photoemission measurements. With this work, by identifying the origins of various defects occurring in perovskite thin films and highlighting importance of designing meaningful and targeted strategies to overcome them, as well as demonstrating sophisticated yet greatly rewarding tools to detect these very nanoscale defect-rich sites, we hope to contribute to development of more viable and durable perovskite photovoltaics
Investigating the Function of Strip1 in Ganglion Cell Survival and Neural Circuit Formation of the Developing Zebrafish Retina
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIn the vertebrate retina, an interplay between retinal ganglion cells (RGCs), amacrine and bipolar cells establishes a synaptic layer called the inner plexiform layer (IPL). This circuit conveys signals from photoreceptors to visual centers in the brain. However, the molecular mechanisms involved in its development remain poorly understood. Striatin-interacting protein 1 (Strip1) is a core component of the STRIPAK complex, and it has shown emerging roles in embryonic morphogenesis. This study uncovers the importance of Strip1 in inner retina development. Using zebrafish, I show that loss of Strip1 causes defects in IPL formation. In strip1 mutants, RGCs undergo dramatic cell death shortly after birth. Cells in the inner nuclear layer subsequently invade the degenerating RGC layer, leading to a disorganized IPL. Mechanistically, zebrafish Strip1 interacts with its STRIPAK partner, Striatin3, to promote RGC survival by suppressing Jun-mediated apoptosis. In addition to its function in RGC maintenance, Strip1 is required for RGC dendritic patterning, which likely promotes interaction between RGCs and amacrine cells for IPL formation. Taken together, I propose that a series of Strip1- mediated regulatory events coordinates inner retinal circuit formation by maintaining RGCs during development, which ensures proper positioning and neurite patterning of inner retinal neurons
Doping Evolution of Magneto-Transport Properties in the Layered Magnetic Semimetal Cr(1+ฮด)Te2
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyLayered magnetic materials are important both from the fundamental perspective of understanding charge, heat, and magnetism as well as from the technological perspective of magnetically enhanced thermoelectric energy generation. Cr(1+ฮด)Te2 is a recently rediscovered magnetic transition metal chalcogenide (TMC) wherein controlling the fraction of Cr (ฮด) systematically tunes the electronic and magnetic properties of this simple binary system. This thesis reports mainly on modulating ฮด to tune the longitudinal thermopower Sxx for different Cr(1+ฮด)Te2 compositions. We show that as the fraction of doped Cr(ฮด) increases between ฮด = 0.3 and ฮด = 0.68, the sign of Sxx changes from positive to negative at a critical doping level of ฮดC โ 0.5. The observed doping-dependent trend in the thermopower is consistent with the evolution of the semimetallic band structure in this material from ARPES, corroborating the electronic tunability of Cr(1+ฮด)Te2 using multiple characterization techniques. Next, an anomalous enhancement in thermoelectric response is also reported around ฮดC, stemming from strong charge-spin coupling. Antiferromagnetic magnons are uncovered as the origin of this thermopower enhancement from analyses of the temperature-dependent magnetothermopower. This picture is further supported by the correspondence of the doping trend of the magnetothermopower with that of the magnetic anisotropy. The findings of this thesis point collectively to the critical nature of the doping level ฮดC in magnetic semimetal Cr1+ฮดTe2. AroundฮดC, near-Fermi-energy pseudogap formation and antiferromagnetic magnons combine to enhance thermoelectric energy conversion in Cr1+ฮดTe2