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Multiexon deletion alleles of ATF6 linked to achromatopsia
Get PDFAchromatopsia (ACHM) is an autosomal recessive disease that results in severe visual loss. Symptoms of ACHM include impaired visual acuity, nystagmus, and photoaversion starting from infancy; furthermore, ACHM is associated with bilateral foveal hypoplasia and absent or severely reduced cone photoreceptor function on electroretinography. Here, we performed genetic sequencing in 3 patients from 2 families with ACHM, identifying and functionally characterizing 2 mutations in the activating transcription factor 6 (ATF6) gene. We identified a homozygous deletion covering exons 8-14 of the ATF6 gene from 2 siblings from the same family. In another patient from a different family, we identified a heterozygous deletion covering exons 2 and 3 of the ATF6 gene found in trans with a previously identified ATF6 c.970C>T (p.Arg324Cys) ACHM disease allele. Recombinant ATF6 proteins bearing these exon deletions showed markedly impaired transcriptional activity by qPCR and RNA-Seq analysis compared with WT-ATF6. Finally, RNAscope revealed that ATF6 and the related ATF6B transcripts were expressed in cones as well as in all retinal layers in normal human retina. Overall, our data identify loss-of-function ATF6 disease alleles that cause human foveal disease.journal articl
On the spillover effect and optimal size of marine reserves for sustainable fishing yields
Get PDFMarine reserves are an essential component of modern fishery management. Marine reserves, which represent a management tradeoff between harvesting and conservation, are fundamental to maintenance of fisheries. Finding optimal reserve sizes that improve fishing yields is not only of theoretical interest, but also of practical importance to facilitate decision making. Also, since the migratory behavior of some species influences the spillover effect of a marine reserve, this is a key consideration when assessing performance of marine reserves. The relationship between optimal reserve size and migration rate/mode has not been well studied, but it is fundamental to management success. Here, I investigate optimal reserve size and its management outcome with different levels of spillover via a simple two-patch mathematical model. In this model, one patch is open to fishing, and the other is closed. The two-patch model is aggregated by single-population dynamics when the migration rate is sufficiently larger than the growth rate of a target species. At this limit, I show that an optimal reserve size exists when pre-reserve fishing occurs at fishing mortality larger than f MSY, the fishing mortality at the maximum sustainable yield (MSY). Also, the fishing yield at an optimal reserve size becomes as large as MSY at the limit. Numerical simulations at various migration rates between the two patches suggest that the maximum harvest under management with a marine reserve is achieved at this limit. This contrasts with the conservation benefit which is maximized at an intermediate migration rate. Numerical simulations show that the above-mentioned condition for an optimal reserve size to exist derived from the aggregated model is necessary when the migration rate is not sufficiently large, and that a moderate migration rate is further necessary for an optimal reserve size to exist. However, high fishing mortality reduces this requirement.journal articl
In Situ Thermometry of a Cold Fermi Gas via Dephasing Impurities
Get PDFThe precise measurement of low temperatures is a challenging, important, and fundamental task for quantum science. In particular, in situ thermometry is highly desirable for cold atomic systems due to their potential for quantum simulation. Here, we demonstrate that the temperature of a noninteracting Fermi gas can be accurately inferred from the nonequilibrium dynamics of impurities immersed within it, using an interferometric protocol and established experimental methods. Adopting tools from the theory of quantum parameter estimation, we show that our proposed scheme achieves optimal precision in the relevant temperature regime for degenerate Fermi gases in current experiments. We also discover an intriguing trade-off between measurement time and thermometric precision that is controlled by the impurity-gas coupling, with weak coupling leading to the greatest sensitivities. This is explained as a consequence of the slow decoherence associated with the onset of the Anderson orthogonality catastrophe, which dominates the gas dynamics following its local interaction with the immersed impurity.journal articl
Infinitesimal Gribov copies in gauge-fixed topological Yang-Mills theories
Get PDFWe study the Gribov problem in four-dimensional topological Yang-Mills theories following the Baulieu-Singer approach in the (anti-)self-dual Landau gauges. This is a gauge-fixed approach that allows to recover the topological spectrum, as first constructed by Witten, by means of an equivariant (or constrained) BRST cohomology. As standard gauge-fixed Yang-Mills theories suffer from the gauge copy (Gribov) ambiguity, one might wonder if and how this has repercussions for this analysis. The resolution of the small (infinitesimal) gauge copies, in general, affects the dynamics of the underlying theory. In particular, treating the Gribov problem for the standard Landau gauge condition in non-topological Yang-Mills theories strongly affects the dynamics of the theory in the infrared. In the current paper, although the theory is investigated with the same gauge condition, the effects of the copies turn out to be completely different. In other words: in both cases, the copies are there, but the effects are very different. As suggested by the tree-level exactness of the topological model in this gauge choice, the Gribov copies are shown to be inoffensive at the quantum level. To be more precise, following Gribov, we discuss the path integral restriction to the Gribov horizon. The associated gap equation, which fixes the so-called Gribov parameter, is however shown to only possess a trivial solution, making the restriction obsolete. We relate this to the absence of radiative corrections in both gauge and ghost sectors. We give further evidence by employing the renormalization group which shows that, for this kind of topological model, the gap equation indeed forbids the introduction of a massive Gribov parameter.journal articl
A genome database for a Japanese population of the larvacean Oikopleura dioica
Get PDFThe larvacean Oikopleura dioica is a planktonic chordate, and is tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of five days make it a promising model organism for developmental biology research. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for three years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 Mb and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named as OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. Moreover, screening of the male-specific scaffolds revealed that over 2.6 Mb of sequence were included in the male-specific Yregion. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.journal articl
Spin–orbit coupling in the presence of strong atomic correlations
Get PDFWe explore the influence of contact interactions on a synthetically spin–orbit coupled system of two ultracold trapped atoms. Even though the system we consider is bosonic, we show that a regime exists in which the competition between the contact and spin–orbit interactions results in the emergence of a ground state that contains a significant contribution from the anti-symmetric spin state. This ground state is unique to few-particle systems and does not exist in the mean-field regime. The transition to this state is signalled by an inversion in the average momentum from being dominated by centre-of-mass momentum to relative momentum and also affects the global entanglement shared between the real- and pseudo-spin spaces. Indeed, competition between the interactions can also result in avoided crossings in the ground state which further enhances these correlations. However, we find that correlations shared between the pseudo-spin states are strongly depressed due to the spin–orbit coupling and therefore the system does not contain spin–spin entanglement.journal articl
Influence of energy gap between charge-transfer and locally excited states on organic long persistence luminescence
Get PDFOrganic long-persistent luminescence (LPL) is an organic luminescence system that slowly releases stored exciton energy as light. Organic LPL materials have several advantages over inorganic LPL materials in terms of functionality, flexibility, transparency, and solution-processability. However, the molecular selection strategies for the organic LPL system still remain unclear. Here we report that the energy gap between the lowest localized triplet excited state and the lowest singlet charge-transfer excited state in the exciplex system significantly controls the LPL performance. Changes in the LPL duration and spectra properties are systematically investigated for three donor materials having a different energy gap. When the energy level of the lowest localized triplet excited state is much lower than that of the charge-transfer excited state, the system exhibits a short LPL duration and clear two distinct emission features originating from exciplex fluorescence and donor phosphorescence.journal articl
Glioma on Chips Analysis of glioma cell guidance and interaction in microfluidic-controlled microenvironment enabled by machine learning
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyIn biosystems, chemical and physical fields established by gradients guide cell migration, which is a fundamental phenomenon underlying physiological and pathophysiological processes such as development, morphogenesis, wound healing, and cancer metastasis. Cells in the supportive tissue of the brain, glia, are electrically stimulated by the local field potentials from neuronal activities. How the electric field may influence glial cells is yet fully understood. Furthermore, the cancer of glia, glioma, is not only the most common type of brain cancer, but the high-grade form of it (glioblastoma) is particularly aggressive with cells migrating into the surrounding tissues (infiltration) and contribute to poor prognosis. In this thesis, I investigate how electric fields in the microenvironment can affect the migration of glioblastoma cells using a versatile microsystem I have developed. I employ a hybrid microfluidic design to combine poly(methylmethacrylate) (PMMA) and poly(dimethylsiloxane) (PDMS), two of the most common materials for microfluidic fabrication. The advantages of the two materials can be complemented while disadvantages can be mitigated. The hybrid microfluidics have advantages such as versatile 3D layouts in PMMA, high dimensional accuracy in PDMS, and rapid prototype turnaround by facile bonding between PMMA and PDMS using a dual-energy double sided tape. To accurately analyze label-free cell migration, a machine learning software, Usiigaci, is developed to automatically segment, track, and analyze single cell movement and morphological changes under phase contrast microscopy. The hybrid microfluidic chip is then used to study the migration of glioblastoma cell models, T98G and U-251MG, in electric field (electrotaxis). The influence of extracellular matrix and chemical ligands on glioblastoma electrotaxis are investigated. I further test if voltage-gated calcium channels are involved in glioblastoma electrotaxis. The electrotaxes of glioblastoma cells are found to require optimal laminin extracellular matrices and depend on different types of voltage-gated calcium channels, voltage-gated potassium channels, and sodium transporters. A reversiblysealed hybrid microfluidic chip is developed to study how electric field and laminar shear can condition confluent endothelial cells and if the biomimetic conditions affect glioma cell adhesion to them. It is found that glioma/endothelial adhesion is mediated by the Ang1/Tie2 signaling axis and adhesion of glioma is slightly increased to endothelial cells conditioned with shear flow and moderate electric field. In conclusion, robust and versatile hybrid microsystems are employed for studying glioma biology with emphasis on cell migration. The hybrid microfluidic tools can enable us to elucidate fundamental mechanisms in the field of the tumor biology and regenerative medicine.doctoral thesi
Metacommunity ecology of Symbiodiniaceae hosted by the coral Galaxea fascicularis
Get PDFCoral−algae symbiosis represents the trophic and structural basis of coral reef ecosystems. However, despite global threats to coral reefs and the dependence of coral health and stress resistance upon such mutualisms, little is known about the community ecology of endosymbiotic Symbiodiniaceae. Concepts and methods from metacommunity ecology may be used to help us understand the assembly and stability of symbiont communities and the mutualisms they comprise. In this study, we sampled colonies of the symbiont-generalist coral Galaxea fascicularis in southwestern Japan and assessed the effects of environmental and host factors on Symbiodinia ceae community composition, while simultaneously exploring residual correlations among symbiont types that may reflect non-random assembly processes such as species interactions. We metabarcoded the Symbiodiniaceae ribosomal internal transcribed spacer 2 (ITS2) region and characterized the endosymbiotic community using 2 different OTU identity cut-offs, and analyzed them with generalized dissimilarity modeling and joint species distribution modeling. We found that Symbiodiniaceae form discrete communities characterized by the dominance of ITS2 types C1, C21a, or D1, that are each associated with a different suite of co-occurring background types and tend to exclude each other in an endosymbiotic community. The communities showed modest responses to temperature, water depth, host genotype, polyp size, and bleaching status, and there was local sequence variation within the ITS2 types. After accounting for the effects of those variables, residual correlations remained in community composition, pointing to the possibility that Symbiodiniaceae community assembly in corals may be structured by interspecific competitive or facilitating interactions rather than only exogenous variables.journal articl
Goal-Directed Behavior under Variational Predictive Coding: Dynamic organization of Visual Attention and Working Memory
Get PDFMental simulation is a critical cognitive function for goal-directed behavior because it is essential for assessing actions and their consequences. When a self-generated or externally specified goal is given, a sequence of actions that is most likely to attain that goal is selected among other candidates via mental simulation. Therefore, better mental simulation leads to better goal-directed action planning. However, developing a mental simulation model is challenging because it requires knowledge of self and the environment. The current paper studies how adequate goal-directed action plans of robots can be mentally generated by dynamically organizing top-down visual attention and visual working memory. For this purpose, we propose a neural network model based on variational Bayes predictive coding, where goal-directed action planning is formulated by Bayesian inference of latent intentional space. Our experimental results showed that cognitively meaningful competencies, such as autonomous top-down attention to the robot end effector (its hand) as well as dynamic organization of occlusion-free visual working memory, emerged. Furthermore, our analysis of comparative experiments indicated that the introduction of visual working memory and the inference mechanism using variational Bayes predictive coding significantly improved the performance in planning adequate goal-directed actions.conference pape