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The Evolution of Ant Mandibles & Advancing Comparative Morphology in 3D
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe diversity of life manifests in the countless forms of organisms, which are a key to understanding natural selection, the interface between genomes and the environment, and functional traits. Ants evolved a broad trophic spectrum and perform vastly different behaviors, universally exhibit a social lifestyle, their range of body plans is highly disparate, and they dominate terrestrial ecosystems. However, despite success in diversification and abundance, we lack an understanding of the factors that promote their morphological diversification or the functional constraints and tradeoffs that incur in ant evolution. In this thesis, I focus on a broad comparative study on the mandibles as the primary tools that ants use in social, environmental, and dietary interactions. I further developed workflows for phenotyping anatomy and spearheaded an initiative, which lays out how to obtain much more standardized 3D anatomical data suitable for automated methods than previously possible. In summary, chapter one of the thesis mainly addresses the solidification of automated muscle analysis based on CT-data. Central to chapter two is Antscan, a pilot project for creating digital libraries of 3D invertebrate anatomy based on high-throughput synchrotron µCT. Based on segmented data for over 600 individual ants, in chapter three, I found that the triangular ant mandible is a ground plan, which ants have mostly retained and remained conservative with. However, convergently evolved shapes driven by functional demands advantageous in predation and division of labor account for overall high morphological diversity. In this thesis, I unraveled contrasts among dimensions of diversity and enabled further research into 3D insect morphology by providing data directly and documenting how to obtain and analyze it and I hope that this work will make a useful contribution to biodiversity science
CREB Mediated Hypoxia Response in Nematostella vectensis
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOxygen availability is hypothesised as one of the critical drivers of metazoan evolution and diversification. The earliest metazoans likely emerged in shallow marine shelves in the Neoproterozoic era, a period characterised by a fluctuating and spatially heterogenous redox environment. This would have imposed physiological constraints on the early animals, selecting for oxygen-responsive and stress-adaptive traits. Understanding how ancestral metazoans navigated these dynamic oxygen landscapes is therefore essential for reconstructing the evolutionary backdrop of the emergence of animal life on Earth. To investigate these mechanisms, the cnidarian Nematostella vectensis, a representative of early-diverging metazoans, is used to comprehensively investigate the molecular and developmental responses to hypoxia stress.
N. vectensis embryogenesis is demonstrated to be oxygen-dependent, with hypoxia inducing a reversible developmental arrest. Transcriptomic profiling reveals an upregulation of cAMP-response element-binding (CREB) family genes and enrichment of CREB signalling pathways under hypoxia. Targeted knockdown of key CREB homologues, followed by hypoxia culture, reveals that CREB activity is essential for coordinating the embryonic response to low oxygen: CREB activation under hypoxia induces the reversible developmental arrest, whereas loss of CREB allows embryos to aberrantly bypass this arrest, producing irreversible defects in endoderm specification. Transcriptomic profiling of CREB knockdown embryos highlights a core CREB-regulated hypoxia-response network enriched for genes involved in extracellular matrix organization, cell–cell adhesion, and tissue architecture. Comparative analysis shows that this CREB-regulated network is deeply conserved across metazoans and non-metazoan lineages.
Together, these findings position CREB as an ancient integrator that couples environmental oxygen availability to morphogenetic events, enhancing developmental robustness during early animal evolution in the fluctuating redox landscapes in Earth’s history
Infection of two cestode larvae, Nybelinia enterika sp. nov. and Phoreiobothrium sp. in oval squid Sepioteuthis lessoniana species complex
Full text linkRecently, oval squid of Sepioteuthis lessoniana species complex has gained importance in aquaculture due to its successful breeding in semi-intensive and intensive aquaculture systems. However, there is a lack of information regarding pathogens and diseases that can affect this species, prompting the need for further research. Two cestode species, Nybelinia enterika sp. nov. and Phoreiobothrium sp., were identified as members of the Trypanorhyncha and Onchoproteocephalidea orders, respectively, using both morphological and molecular diagnostic markers in wild-caught oval squids (Sepioteuthis lessoniana sp.1, S. lessoniana sp.2, S. lessoniana sp.3). These cestode species were found to use the oval squids as intermediate hosts. In histopathology samples, the infected squid with N. enterika was surrounded by numerous hemocytes in the infected area. In the genomes of both cestode species, we identified multiple genes for enzymes involved in cephalopod tissue degradation, such as cysteine proteases including cathepsin-L, cathepsin-D, cathepsin-A, cathepsin-B, cathepsin-K, and cathepsin-S. These enzymes potentially help the parasites manipulate the squid immune system and neutralize squid hemocytes. The detection of these parasites in wild squid populations, with 100% prevalence in Okinawa, is concerning as the effect of these parasites on human consumers’ health remains unknown. However, our research demonstrated that fully cultured squid remain completely cestode parasite-free, indicating they are more likely to meet the highest standards for food safety and quality
Biologically Plausible Synaptic Plasticity Model for Rapid Neuronal Tuning
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIn the intricate workings of the brain, neurons play a fundamental role in detecting meaningful patterns amidst a constant stream of information. However, the rapidity with which neurons accomplish this task often goes unnoticed in computational models, leading to a gap in understanding crucial mechanistic features observed in biological neurons. To bridge this gap, I introduce a class of neural models equipped with a biologically-inspired synaptic plasticity rule. The aim of this thesis research is to shed light on the brain’s ability to rapidly learn and discern statistically salient patterns. My approach leverages the dynamic interplay between neural activity and synaptic plasticity, where somatic spikes propagate back to dendrites, facilitating self-supervised detection and learning of presynaptic neuron communities impinging on dendrites. I showcase the efficacy of these models in various tasks, including pattern recognition and spatial navigation, where they establish swift associations between behavior and environmental cues. Moreover, in exploring multi-compartmental neural architectures, I extend the synaptic plasticity rule to elucidate the initiation and development of local dendritic spikes, offering insights into neural processing mechanisms. My modeling work underscores the importance of pre-existing neural assemblies in robust pattern learning within recurrent networks. By illuminating the self-supervision function of backpropagating action potentials and the role of pre-existing neural assemblies, my findings contribute to a deeper comprehension of brain cognitive function and its implications for artificial intelligence and neuroscience
Effects of Incompatible Distortion Rates in Fluid Dynamics
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe aim of this research is to investigate developments arising from permitting the distortion rate in a fluid to be the sum of two smooth components — both inherently incompatible, as they do not represent gradients of vector fields. This gives rise to a set of two coupled evolution equations. One of these equations generalizes the Navier–Stokes equation for an incompressible fluid. The other equation governs a tensor field that characterizes any incompatibility that is present. We build on the theory of incompatible flows introduced by Fosdick and Fried [1], who analyzed Poiseuille flow in a rectangular channel. This study presents findings that focus on the application of the framework to Poiseuille–Couette flow, where the boundary condition is modified to include a moving upper wall, as well as to pipe flow with a circular annular cross-section, where we investigate the effects of geometry. In each of the generalizations considered, we identify the emergence of coexistent compatible and incompatible flows. This phenomenon is distinct from that observed in plane Poiseuille flow. We propose that this coexistence is analogous to the transitional state between laminar and turbulent flow, where both flow states can exist simultaneously under certain conditions, marking a regime of transition between two distinct behaviors. The plug-like behavior seen in our flow dynamics exhibits similarities to what is observed in turbulent fluid flow. To deepen our analysis, we compare our velocity profile results with direct numerical simulation (DNS) data, revealing critical insights into the flow characteristics and underlying mechanisms governing the observed phenomena
On the Analysis of Collective Dynamics in Social Groups with Bees and Football Players as Case Studies
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe main focus of this thesis is investigating the emergent effects observed in the collective dynamics of the honeybee hive. We use a previously acquired dataset of time-resolved trajectories of hundreds of bees inside the hive, recorded for multiple days and nights. In a series of papers, we study the temporal and spatial dynamics of the bee hive, uncovering scale-free correlations of occupancy fluctuations in both temporal and spatial domains. These observations indicate the proximity of the system to the second-order phase transition. Furthermore, we observe a non-trivial relationship between throughput and density, implying that the beehive undergoes a jamming transition. This finding is explored further by constructing a model of jamming in 2D using stochastic cellular automata and exploring how correlation length is dependent on the density. Additional insights are obtained by studying the properties of the functional network computed using correlations between the timeseries of individual bees.
The supplementary project is centered on the study of the trajectories of professional football players from the Japanese football league. It has been found that statistical properties of trajectories of individual players’ are best described by the Lévy walk dynamics. Furthermore, we have found that these dynamics are preserved when centers of mass trajectories for each team are considered. However, the power-law distribution of step sizes which is indicative of the Lévy walk is reduced to the exponential when only the periods when players are in possession of the ball are considered. Based on these findings we hypothesize that players’ behavior is reminiscent of that of the foraging animals which resort to Lévy walk when resource distribution is sparse
Comprehensive Identification of Plasma Membrane Repair Proteins Uncovered the Clathrin-mediated Endocytosis-dependent Repair Protein Delivery Mechanisms
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyDamage to the plasma membrane (PM) is common in living cells. Virtually all cells have mechanisms to repair the damaged PM. One of the evolutionarily conserved PM repair processes is targeting proteins, defined as PM repair proteins, to the damage site. PM repair proteins play critical roles in the PM repair processes. However, the mechanisms underlying the repair protein delivery to the damage site are largely unexplored. Moreover, identifying new repair proteins remains challenging in this field. In this thesis, I addressed these issues using budding yeast Saccharomyces cerevisiae as a model. In the first project, I revealed that clathrin-mediated trafficking of phospholipid flippases is required for PM/cell wall repair in budding yeast. In addition, the deletion of phospholipid flippases impaired the accumulation of exocyst, which functions to dock exocytic vesicles with the PM at the damage site. I propose the model that phospholipid flippases remodel the lipid composition at the damage site, thereby facilitating the binding of exocyst to the PM.
In the second project, I performed a high-throughput visual screening using yeast GFP collections, which cover ~90 % (5,718 ORFs) of yeast ORFs to comprehensively identify the repair proteins. I identified 564 proteins whose localization changed in response to the PM-damaging chemical SDS. The laser damage assay identified 80 proteins accumulated at the damage site, including 72 previously unidentified repair protein candidates. By quantifying the fluorescence intensity at the damage site over time, I revealed the functional order of repair proteins. Among the identified repair proteins, those involved in clathrin-mediated endocytosis (CME) were required for yeast growth in conditions that induce PM/cell wall damage. I found that CME proteins are required for polarized exocytosis at the damage site and for the transportation of PM proteins from the growing bud site to the damage site. In addition, one of the CME cargoes, Snc1, was recovered from the damage site to the growing bud site, presumably via CME. Given that these processes occur from 2min after the damage, CME may restructure the damaged PM after resealing. I propose the model that CME restructures the damaged PM by regulating the amount of PM proteins at the damage site
Cholinergic Interneurons of the Dorsomedial Striatum Mediate Winner-Loser Effects on Social Hierarchy Dynamics in Male Mice
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyThe overall aim of the research reported in this thesis is to investigate the phenomena and putative mechanisms of flexibility in the social hierarchy of male mice (C57BL7/J and heterozygous ChAT-cre mice). A social hierarchy is an organization of individuals by rank that occurs in social animals. Establishing a new social hierarchy involves flexible behavior in deciding, when competing with other animals, whether to be a winner or loser, responding to the experience of winning or losing, and subsequent stabilization of rank. The neural circuits underlying such flexible behavior have yet to be fully understood. Previous research indicates that cholinergic interneurons in the dorsomedial striatum play a role in various forms of behavioral flexibility. I hypothesize that similar mechanisms may be involved in social hierarchy dynamics. To investigate the effects of the experience of winning and losing on the social hierarchy, I used the dominance tube test to measure ranking within group housed mice, before and after between-cage competitions using the same test. I found that the experience of winning or losing against mice from different cages not only contributes to new social hierarchies among the competitors, but also causally influences the subsequent social hierarchy among their cage mates in the home cage – supporting the hypothesis of winner-loser effects on later social ranking. To test the hypothesis that cholinergic interneurons contribute to social hierarchy dynamics, I made a selective lesion of cholinergic interneurons in the dorsomedial striatum. The lesion did not prevent social hierarchy formation among pairs of similarly ranked individuals from different cages. However, it reduced the loser effect of external competition on the subsequent home-cage rankings in dominant mice. These findings support the concept of winner-loser effects on subsequent competition, and which suggest that cholinergic interneurons in dorsomedial striatum increase the flexibility of social hierarchy dynamics
Critical Role of YTHDF2 and CCR4-NOT Complex in Pancreatic β-cell Homeostasis
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyPancreatic β-cells synthesize and secrete insulin to maintain blood glucose levels within a normal range. Decreased insulin secretion and β-cell mass, as well as β-cell dedifferentiation, are observed in type 2 diabetes patients. Thus, maintaining β-cell function and identity is important for glucose homeostasis. Recent studies have shown that the N6-methyladenosine (m6A) methylation level in mRNA is reduced in the islets of patients with type 2 diabetes. m6Amethylated mRNAs are recognized by m6A-binding proteins, which play pivotal roles in various aspects of mRNA processing and metabolism. However, the signaling pathways regulating β- cell homeostasis via m6A modification remain incompletely understood. One of the m6Abinding proteins, YTHDF2, promotes mRNA degradation by recruiting the CCR4-NOT deadenylase complex. This study demonstrates that impaired mRNA turnover via YTHDF2 and the CCR4-NOT complex disrupts β-cell homeostasis. These findings suggest that the degradation of mRNAs in pancreatic β-cells is cooperatively regulated by YTHDF2 and the CCR4-NOT complex, ensuring the maintenance of β-cell function and identity. Furthermore, integrative omics analyses revealed specific mRNAs degraded through this pathway. The genes identified in this study may serve as potential therapeutic targets for type 2 diabetes treatment
From Bottom to Top Interfaces and Layers: the Holistic Engineering Approach for Efficient, Stable and Large-Area n-i-p Structured Perovskite Solar Cells
Full text linkOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyMetal halide perovskites have emerged rapidly as promising materials for solar energy harvesting, with perovskite solar cell (PSC) power conversion efficiencies (PCEs) reaching 27%. Despite their excellent optoelectronic properties, low production cost, and facile up-scalability, the commercialization of perovskite solar modules (PSMs) still faces challenges in achieving long-term stable and large-area devices. This thesis focuses on optimizing the widely used n-i p architecture, where the bottom electron transport layer (ETL) is coated with the perovskite light-absorber, followed by a hole transport layer (HTL). For ensuring the stability of metal oxides layer used in HTL and ETL as bottom layers against the solution processed perovskite layer deposition, different metal oxides and perovskite compositions were well studied to understand and develop strategies for protecting the bottom metal oxide. To achieve a uniform large-area perovskite layer, the hybrid-chemical-vapor-deposition (HCVD) method was explored for perovskite film deposition. In addition, the perovskite seeding and coordination solvent engineering strategies were incorporated to improve crystallinity, facilitate the growth of larger grains, and promote the full conversion of the inorganic lead species during film growth. Furthermore, the HCVD method was extended to inorganic perovskite films. By using vapor amine molecules to mediate the formation of low-dimensional perovskite intermediate phases from CsPbI3, the crystallinity and orientation of CsPbI3 were enhanced, and it was scalable for fabricating large-area modules. A surface passivation strategy based on a hydrophobic molecule of perfluorobutanesulfonyl chloride (PFSC) was developed for CsPbI3-based PSMs, which passivates the perovskite surface, enhances interfacial contact with HTL, adjusts energy levels, and reduces surface defects, resulting in PSMs with a high certified efficiency and prolonged device operation lifetime. To further enhance PSM stability, the conventional 2,2’,7,7- tetrakis(N,N-di(4-methoxyphenylamine)-9,9’-spirobifluorene (spiro-OMeTAD, spiro) based HTL was modified. The commonly employed additive of lithium bis(trifluoromethane)sulfonimide (LiTFSI) was replaced by ammonia bis(trifluoromethane)sulfonimide (NH4TFSI), and a light-oxidation doping treatment was developed to improve the oxidation process in solution. This method avoids the time-consuming post-oxidation step in spiro-HTL in n-i-p devices. This study also examined the beneficial effects of TFSI salts in forming low-dimensional (2D) perovskite structures with enhanced thermal stability and prolonged device lifetime