著者

Tomoko Mihara Hitoshi Koyano Pascal Hingamp Nigel Grimsley Susumu Goto Hiroyuki Ogata

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME17203, (Released:2018-05-25)

被引用文献数

80

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Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family “Megaviridae”, suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early “Big-Bang” radiation of the eukaryotic tree of life.

著者

Masaaki Kotera Susumu Goto

出版者

一般社団法人 日本生物物理学会

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

vol.13, pp.195-205, 2016 (Released:2016-07-15)

参考文献数

86

被引用文献数

15

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Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies, i.e., reference-based vs. de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predicted de novo from chemical transformations of the putative substrate-product pair. This review summarizes studies involving reference-based and de novo metabolic pathway reconstruction and discusses the importance of the classification and structure-function relationships of enzymes.

著者

Yutaro MOTOORI Susumu GOTO

出版者

The Japan Society of Mechanical Engineers

雑誌

Journal of Fluid Science and Technology (ISSN:18805558)

巻号頁・発行日

vol.14, no.3, pp.JFST0016, 2019 (Released:2019-12-19)

参考文献数

16

被引用文献数

3

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Coarse-graining is indispensable for extracting a hierarchy of vortices in fully developed turbulent flow with multiscale nature. In the present study, for a high-Reynolds-number turbulent boundary layer, we employ two simple coarse-graining methods in real space; namely, a Gaussian filter and the combination of the Gaussian filters at two scales. The former corresponds to a low-pass filter of Fourier modes, while the latter corresponds to a band-pass filter. We also examine two different filter widths for the band-pass filter. Then, we show difference in the statistics of the three filtered fields. Since the velocity gradients in turbulence are mainly determined by the smallest-scale motions, vortical structures identified by the second invariant Q of the velocity gradient coarse-grained by the filters are similar. However, there is difference between low- and band-pass filtered fields in the contribution to the enstrophy production rates. This is because the production rates are determined not only by the magnitude of the strain rates but also by the alignment between the vorticity and the stretching direction. In addition, since vortices are not created in the entire system, the conditional sampling by the value of Q is essential to understand the generation mechanism of the hierarchy of vortices. The conditional analysis of the band-pass filtered fields demonstrates that small-scale vortices in the log layer are stretched by twice-larger vortices, whereas they weaken the twice-larger vortices. This observation is consistent with the picture of the energy cascade. We also show that when using the band-pass filter, these conclusions are robust irrespective of the choice of the filter width.