KEIO RESEARCHERS INFORMATION SYSTEM

Papers 【 Display / hide 】

Papers 【 Display / hide 】

• A global metagenomic map of urban microbiomes and antimicrobial resistance

  D Danko, D Bezdan, EE Afshin, S Ahsanuddin, C Bhattacharya, DJ Butler, ...

  Cell 184 (13), 3376-3393.e17 （Cell)  184 （ 13 ） 3376 - 3393.e17 2021

  ISSN  00928674

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  We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

  • Access to Document (DOI)

• On the influence of biomimetic shark skin in dynamic flow separation

  P Guo, K Zhang, Y Yasuda, W Yang, J Galipon, DE Rival

  Bioinspiration & Biomimetics 16 (3), 034001 （Bioinspiration and Biomimetics)  16 （ 3 ）  2021

  ISSN  17483182

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  The effect of shark skin on the boundary-layer separation process under dynamic conditions (maneuvers) has been studied experimentally. We use a foil covered with biomimetic shark skin to explore how this type of surface impacts boundary-layer dynamics in both steady and accelerating conditions. The effect of denticles is assessed via particle image velocimetry in the wake. It is shown that dynamic conditions and small-scale disturbances can mitigate boundary-layer separation through instantaneous modification of the local pressure-gradient distribution. For instance, the region of favourable pressure gradient can be extended by accelerating the foil. The acceleration results in a thinner separated shear layer on the foil surface when compared to the steady reference case. This remarkable difference indicates that local roughness (introduced through for instance biomimetic shark skin) may trigger an interaction with relatively large-scale structures in the boundary layer for effective boundary-layer control during unsteady propulsion and maneuvering.

  • Access to Document (DOI)

• Correlative microscopy and block-face imaging (CoMBI) method for both paraffin-embedded and frozen specimens

  N Ishii, Y Tajika, T Murakami, J Galipon, H Shirahata, R Mukai, D Uehara, ...

  Scientific Reports 11 (1), 1-17 （Scientific Reports)  11 （ 1 ）  2021

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  Correlative microscopy and block-face imaging (CoMBI), a method that we previously developed, is characterized by the ability to correlate between serial block-face images as 3-dimensional (3D) datasets and sections as 2-dimensional (2D) microscopic images. CoMBI has been performed for the morphological analyses of various biological specimens, and its use is expanding. However, the conventional CoMBI system utilizes a cryostat, which limits its compatibility to only frozen blocks and the resolution of the block-face image. We developed a new CoMBI system that can be applied to not only frozen blocks but also paraffin blocks, and it has an improved magnification for block-face imaging. The new system, called CoMBI-S, comprises sliding-type sectioning devices and imaging devices, and it conducts block slicing and block-face imaging automatically. Sections can also be collected and processed for microscopy as required. We also developed sample preparation methods for improving the qualities of the block-face images and 3D rendered volumes. We successfully obtained correlative 3D datasets and 2D microscopic images of zebrafish, mice, and fruit flies, which were paraffin-embedded or frozen. In addition, the 3D datasets at the highest magnification could depict a single neuron and bile canaliculus.

  • Access to Document (DOI)

• Complete Genome Sequence of Sphingomonas paucimobilis Strain Kira, Isolated from Human Neuroblastoma SH-SY5Y Cell Cultures Supplemented with Retinoic Acid

  K Nishimura, M Ikarashi, Y Yasuda, M Sato, M Cano Guerrero, J Galipon, ...

  Microbiology Resource Announcements 10 (6), e01156-20 （Microbiology Resource Announcements)  10 （ 6 ）  2021

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  Because of its small size, Gram-negative Sphingomonas paucimobilis can pose a risk of nosocomial infection. We report the complete circular genome sequence of S. paucimobilis strain Kira, which was isolated from retinoic acid-supplemented SHSY5Y human cell cultures, to be 3,917,410bp (G1Ccontent,65.7%; 3,672 protein-coding sequences), with two plasmids (79,575bp and 44,333bp).

  • Access to Document (DOI)

• Complete Genome Sequence of Halomonas hydrothermalis Strain Slthf2, a Halophilic Bacterium Isolated from a Deep-Sea Hydrothermal-Vent Environment

  N Takeyama, M Huang, K Sato, J Galipon, K Arakawa

  Microbiology resource announcements 9 (15), e00294-20 （Microbiology Resource Announcements)  9 （ 15 ）  2020

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  Halomonas hydrothermalis strain Slthf2 is a Gram-negative bacterium isolated from low-temperature hydrothermal fluids in South Pacific Ocean vent fields located at 2,580-m depth. Here, we report the complete genome sequence of this strain, which has a genome size of 4.12 Mb, with a GC content of 53.2%.

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Courses Taught 【 Display / hide 】

Courses Taught 【 Display / hide 】

• GENETIC ENGINEERING LABORATORY

  2024

• GENETIC ENGINEERING LABORATORY

  2023

• GENETIC ENGINEERING LABORATORY

  2022

• GENETIC ENGINEERING LABORATORY

  2021

• GENETIC ENGINEERING LABORATORY

  2020

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