VCGIDB: A database and web resource for the genomic islands from Vibrio cholerae

Vibrio cholerae is the causative agent of cholera, which is a severe, life-threatening diarrheal disease. The current seventh pandemic has not been eradicated and the outbreak is still ongoing around the world. The evolution of the pandemic-causing strain has been greatly influenced by lateral gene transfer, and the mechanisms of acquisition of pathogenicity in V. cholerae are mainly involved with genomic islands (GIs). Thus, detecting GIs and their comprehensive information is necessary to understand the continuing resurgence and newly emerging pathogenic V. cholerae strains. In this study, 798 V. cholerae strains were tested using the GI-Scanner algorithm, which was developed to detect candidate GIs and identify them in a comparative genomics approach. The algorithm predicted 435 highly possible genomic islands, and we built a database, called Vibrio cholerae Genomic Island Database (VCGIDB). This database shows advanced results that were acquired from a large genome set using phylogeny-based predictions. Moreover, VCGIDB is a highly expendable database that does not require intensive computation, which enables us to update it with a greater number of genomes using a novel genomic island prediction method. The VCGIDB website allows the user to browse the data and presents the results in a visual manner.

Improving Neural Radiance Field using Near-Surface Sampling with Point Cloud Generation

Neural radiance field (NeRF) is an emerging view synthesis method that samples points in a three-dimensional (3D) space and estimates their existence and color probabilities. The disadvantage of NeRF is that it requires a long training time since it samples many 3D points. In addition, if one samples points from occluded regions or in the space where an object is unlikely to exist, the rendering quality of NeRF can be degraded. These issues can be solved by estimating the geometry of 3D scene. This paper proposes a near-surface sampling framework to improve the rendering quality of NeRF. To this end, the proposed method estimates the surface of a 3D object using depth images of the training set and sampling is performed around there only. To obtain depth information on a novel view, the paper proposes a 3D point cloud generation method and a simple refining method for projected depth from a point cloud. Experimental results show that the proposed near-surface sampling NeRF framework can significantly improve the rendering quality, compared to the original NeRF and a state-of-the-art depth-based NeRF method. In addition, one can significantly accelerate the training time of a NeRF model with the proposed near-surface sampling framework.Comment: 13 figures, 2 table

Quantitative agreement of Dzyaloshinskii-Moriya interactions for domain-wall motion and spin-wave propagation

The magnetic exchange interaction is the one of the key factors governing the basic characteristics of magnetic systems. Unlike the symmetric nature of the Heisenberg exchange interaction, the interfacial Dzyaloshinskii-Moriya interaction (DMI) generates an antisymmetric exchange interaction which offers challenging opportunities in spintronics with intriguing antisymmetric phenomena. The role of the DMI, however, is still being debated, largely because distinct strengths of DMI have been measured for different magnetic objects, particularly chiral magnetic domain walls (DWs) and non-reciprocal spin waves (SWs). In this paper, we show that, after careful data analysis, both the DWs and SWs experience the same strength of DMI. This was confirmed by spin-torque efficiency measurement for the DWs, and Brillouin light scattering measurement for the SWs. This observation, therefore, indicates the unique role of the DMI on the magnetic DW and SW dynamics and also guarantees the compatibility of several DMI-measurement schemes recently proposed.Comment: 24 pages, 5 figure

The IMPDH cytoophidium couples metabolism and fetal development in mice

The cytoophidium is an evolutionarily conserved subcellular structure formed by filamentous polymers of metabolic enzymes. In vertebrates, inosine monophosphate dehydrogenase (IMPDH), which catalyses the rate-limiting step in guanosine triphosphate (GTP) biosynthesis, is one of the best-known cytoophidium-forming enzymes. Formation of the cytoophidium has been proposed to alleviate the inhibition of IMPDH, thereby facilitating GTP production to support the rapid proliferation of certain cell types such as lymphocytes, cancer cells and pluripotent stem cells (PSCs). However, past studies lacked appropriate models to elucidate the significance of IMPDH cytoophidium under normal physiological conditions. In this study, we demonstrate that the presence of IMPDH cytoophidium in mouse PSCs correlates with their metabolic status rather than pluripotency. By introducing IMPDH2 Y12C point mutation through genome editing, we established mouse embryonic stem cell (ESC) lines incapable of forming IMPDH polymers and the cytoophidium. Our data indicate an important role of IMPDH cytoophidium in sustaining a positive feedback loop that couples nucleotide biosynthesis with upstream metabolic pathways. Additionally, we find that IMPDH2 Y12C mutation leads to decreased cell proliferation and increased DNA damage in teratomas, as well as impaired embryo development following blastocoel injection. Further analysis shows that IMPDH cytoophidium assembly in mouse embryonic development begins after implantation and gradually increases throughout fetal development. These findings provide insights into the regulation of IMPDH polymerisation in embryogenesis and its significance in coordinating cell metabolism and development

Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK‐14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.

Development of Highly Reliable Power and Communication System for Essential Instruments Under Severe Accidents in NPP

AbstractThis article proposes a highly reliable power and communication system that guarantees the protection of essential instruments in a nuclear power plant under a severe accident. Both power and communication lines are established with not only conventional wired channels, but also the proposed wireless channels for emergency reserve. An inductive power transfer system is selected due to its robust power transfer characteristics under high temperature, high pressure, and highly humid environments with a large amount of scattered debris after a severe accident. A thermal insulation box and a glass-fiber reinforced plastic box are proposed to protect the essential instruments, including vulnerable electronic circuits, from extremely high temperatures of up to 627°C and pressure of up to 5 bar. The proposed wireless power and communication system is experimentally verified by an inductive power transfer system prototype having a dipole coil structure and prototype Zigbee modules over a 7-m distance, where both the thermal insulation box and the glass-fiber reinforced plastic box are fabricated and tested using a high-temperature chamber. Moreover, an experiment on the effects of a high radiation environment on various electronic devices is conducted based on the radiation test having a maximum accumulated dose of 27 Mrad