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Biogenesis of Type V pili
Get PDFPili or fimbriae, which are filamentous structures present on the surface of bacteria, were purified from a periodontal pathogen, Porphyromonas gingivalis, in 1980s. The protein component of pili (stalk pilin), which is its major component, was named FimA; it has a molecular weight of approximately 41 kDa. Because the molecular weight of the pilin from P. gingivalis is twice that of pilins from other bacterial pili, the P. gingivalis Fim pili were suggested to be formed via a novel mechanism. In earlier studies, we reported that the FimA pilin is secreted on the cell surface as a lipoprotein precursor, and the subsequent N‐terminal processing of the FimA precursor by arginine‐specific proteases is necessary for Fim pili formation. The crystal structures of FimA and its related proteins were determined recently, which show that Fim pili are formed by a protease‐mediated strand‐exchange mechanism. The most recent study conducted by us, wherein we performed cryoelectron microscopy of the pilus structure, provided evidence in support of this mechanism. As the P. gingivalis Fim pili are formed through novel transport and assembly mechanisms, such pili are now designated as Type V pili. Surface lipoproteins, including the anchor pilin FimB of Fim pili that are present on the outer membrane, have been detected in certain Gram‐negative bacteria. Here, we describe the assembly mechanisms of pili, including those of Type V and other pili, as well as the lipoprotein transport mechanisms.journal articl
Emergence of nematic paramagnet via quantum order-by-disorder and pseudo-Goldstone modes in Kitaev magnets
Get PDFThe appearance of nontrivial phases in Kitaev materials exposed to an external magnetic field has recently been a subject of intensive studies. Here, we elucidate the relation between the field-induced ground states of the classical and quantum spin models proposed for such materials, by using the infinite density matrix renormalization group (iDMRG) and the linear spin wave theory (LSWT). We consider the KΓΓ′ model, where Γ and Γ′ are off-diagonal spin exchanges on top of the dominant Kitaev interaction K. Focusing on the magnetic field along the [111] direction, we explain the origin of the nematic paramagnet, which breaks the lattice-rotational symmetry and exists in an extended window of magnetic field, in the quantum model. This phenomenon can be understood as the effect of quantum order-by-disorder in the frustrated ferromagnet with a continuous manifold of degenerate ground states discovered in the corresponding classical model. We compute the dynamical spin structure factors using a matrix operator based time evolution and compare them with the predictions from LSWT. We, thus, provide predictions for future inelastic neutron scattering experiments on Kitaev materials in an external magnetic field along the [111] direction. In particular, the nematic paramagnet exhibits a characteristic pseudo-Goldstone mode, which results from the lifting of a continuous degeneracy via quantum fluctuations.journal articl
The Milstein Bipyridyl PNN Pincer Complex of Ruthenium Becomes a Noyori-Type Catalyst under Reducing Conditions
Get PDFHydrogenation of the dearomatized PNN ligand of the Milstein bipyridyl complex RuH(CO)[PNN] (2) gives a square-pyramidal Ru(II) product RuH(CO)[pPNN] (5). The central ring of the pPNN ligand is a piperidine. A minor byproduct of the hydrogenation reaction is complex 6 which has a dimeric structure made of two Ru(II) fragments each possessing a partly hydrogenated PNN ligand. The structures of 5 and 6 have been elucidated by NMR spectroscopy and X-ray crystallography. The PNN ligand of 2 is also hydrogenated under the conditions of the catalytic dehydrogenative coupling of ethanol to ethyl acetate. No direct evidence of the aromatized dihydride RuH2(CO)[PNN] (4) was found in this study. However, treating RuHCl(CO)[PNN] with Li[HBEt3] or reacting 2 with H2 at low temperature resulted in a structurally characterized hydride-bridged dimer (7) bearing intact aromatized bipyridyl ligands. M06-L/def2-QZVP DFT calculations provided insights into the thermodynamics of the stoichiometric reactions of this work and into the nature of the intermediates of the catalytic ester hydrogenation facilitated by RuH2(CO)[pPN(H)N] (8) formed from 5 under H2.journal articl
Spontaneous and stimulus-induced coherent states of critically balanced neuronal networks
Get PDFHow the information microscopically processed by individual neurons is integrated and used in organizing the behavior of an animal is a central question in neuroscience. The coherence of neuronal dynamics over different scales has been suggested as a clue to the mechanisms underlying this integration. Balanced strong excitation and inhibition may amplify microscopic fluctuations to a macroscopic level, thus providing a mechanism for generating coherent multiscale neuronal dynamics. Previous theories of brain dynamics, however, were restricted to cases in which inhibition dominated excitation and suppressed fluctuations in the macroscopic population activity. In the present study, we investigate the dynamics of neuronal networks at a critical point between excitation-dominant and inhibition-dominant states. In these networks, the microscopic fluctuations in neuronal activities are amplified by the strong excitation and inhibition to drive the macroscopic dynamics, while the macroscopic dynamics determine the statistics of the microscopic fluctuations. Developing a novel type of mean-field theory applicable to this class of interscale interactions, for which an analytical approach has previously been unknown, we show that the amplification mechanism generates spontaneous, irregular macroscopic rhythms similar to those observed in the brain. Through the same mechanism, microscopic inputs to a small number of neurons effectively entrain the dynamics of the whole network. These network dynamics undergo a probabilistic transition to a coherent state, as the magnitude of either the balanced excitation and inhibition or the external inputs is increased. Our mean-field theory successfully predicts the behavior of this model. Furthermore, we numerically demonstrate that the coherent dynamics can be used for state-dependent read-out of information from the network. These results show a novel form of neuronal information processing that connects neuronal dynamics on different scales, advancing our understanding of the circuit mechanisms of brain computing.journal articl
Functional Analysis of CCR4-NOT Complex in Pancreatic β Cell
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyFunctional analysis of CCR4-NOT complex in pancreatic β cell
Pancreatic β cells are responsible for production and secretion of insulin in response to increasing blood glucose levels. Therefore, defects in pancreatic β cell function lead to hyperglycemia and diabetes mellitus. While extensive research has focused on signaling, transcriptional, and epigenetic regulation in β cells, how post-transcriptional mechanisms influence the β cell gene expression program is largely unknown. The carbon catabolite repression 4 (CCR4)–negative on TATA-less (NOT) complex (CCR4-NOT complex), a major deadenylase conserved in eukaryotes, catalyzes mRNA deadenylation which is the rate limiting step in mRNA decay pathway. The CCR4-NOT complex has been implicated in the development of metabolic diseases. However, whether the CCR4-NOT complex affects β cell function is not addressed. In this thesis, I aim to understand the importance of post-transcriptional regulation in β cells by generating mice lacking the Cnot3 gene, which encodes an essential CCR4-NOT complex subunit, in β cells. Suppression of CNOT3 in β cells caused β cell dysfunction and diabetes. This was associated with the decreased expression of β cell-specific genes and increased expression of genes specifically repressed in β cells, called “β cell disallowed genes”. By combining whole transcriptome and proteome analyses and subsequent validations using quantitative PCR (qPCR) and immunoblot analyses, I found that mRNA and protein expression patterns were largely different from normal β cells upon CNOT3 suppression, which was clearly relevant to the observed phenotypes. I also found that some β cell disallowed genes were stabilized in the absence of CNOT3, suggesting that their expression was maintained at low levels under the control of the CCR4-NOT complex. Together, this study uncovered mRNA deadenylation by CCR4-NOT complex as a novel molecular mechanism by which β cell identity and function are regulated.doctoral thesi
Small-scale universality in the spectral structure of transitional pipe flows
Get PDFTurbulent flows are not only everywhere, but every turbulent flow is the same at small scales. The extraordinary simplification engendered by this "small-scale universality" is a hallmark of turbulence theory. However, on the basis of the restrictive assumptions invoked by A. N. Kolmogorov to demonstrate this universality, it is widely thought that only idealized turbulent flows conform to this framework. Using experiments and simulations that span a wide range of Reynolds number, we show that small-scale universality governs the spectral structure of a class of flows with no apparent ties to the idealized flows: transitional pipe flows. Our results not only extend the universality of Kolmogorov's framework beyond expectation but also establish an unexpected link between transitional pipe flows and Kolmogorovian turbulence.journal articl
Turbine Characteristics of Wave Energy Conversion Device for Extraction Power Using Breaking Waves
Get PDFA new type of wave energy converter which harnesses electricity from onshore breaking waves has been studied at Okinawa Institute of Science and Technology Graduate University (OIST) since 2014. This concept has been demonstrated at a coral beach on the Maldives since 2018. Wave energy conversion is possible when waves approaching the shore steepen due to decreased water depth resulting in wave breaks near the surface. A steepened wave reaches the critical velocity of 4~6 m/sec shoreward before it breaks. A rotating blade takes advantage of this breaking phenomenon to convert the wave energy into electricity. The work presented here includes an experimental and numerical investigation of a prototype model of the wave energy converter. The turbine having five blades of variable chord lengths, twist angles, and constant thickness profile from hub to tip was simulated under similar flow as well as testing conditions, to predict the turbine performance. A commercial computational fluid dynamic tool SolidWorks Flow Simulation 2018 was used for the simulations at various rotation speeds with a uniform inlet velocity. The modified k-ε with a two-scale wall function turbulence closure model was selected. The validation performed for different test cases showed that the present computational results match in good agreement with the experimental results. Additionally, details performance of the turbine running, and generator characteristics have been reported in this paper.journal articl
High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities
Get PDFLarge-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.journal articl
Numerical simulations of vorticity banding of emulsions in shear flows
Get PDFMultiphase shear flows often show banded structures that affect the global behavior of complex fluids e.g. in microdevices. Here we investigate numerically the banding of emulsions, i.e. the formation of regions of high and low volume fractions, alternated in the vorticity direction and aligned with the flow (shear bands). These bands are associated with a decrease of the effective viscosity of the system. To understand the mechanism of experimentally observed banding, we have performed interface-resolved simulations of the two-fluid system. The experiments were performed starting with a random distribution of droplets, which under the applied shear, evolve in time resulting in a phase separation. To numerically reproduce this process, the banded structures are initialized in a narrow channel confined by two walls moving in opposite directions. We find that the initial banded distribution is stable when droplets are free to merge and unstable when coalescence is prevented. In this case, additionally, the effective viscosity of the system increases, resembling the rheological behavior of suspensions of deformable particles. Droplet coalescence, on the other hand, allows emulsions to reduce the total surface of the system and, hence, the energy dissipation associated with the deformation, which in turn reduces the effective viscosity.journal articl
