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Al-Shayeb, B.*; Sachdeva, R.*; Chen, L.-X.*; Ward, F.*; Munk, P.*; Devoto, A.*; Castelle, C. J.*; Olm, M. R.*; Bouma-Gregson, K.*; 天野 由記; et al.
Nature, 578(7795), p.425 - 431, 2020/02
被引用回数：220 パーセンタイル：99.5(Multidisciplinary Sciences)Phage typically have small genomes and depend on their bacterial hosts for replication. We generated metagenomic datasets from many diverse ecosystems and reconstructed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, initiation and elongation factors and ribosomal proteins. Phage CRISPR have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. Some phage repurpose bacterial systems for phage-defense to eliminate competing phage. We phylogenetically define seven major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that large gene inventories reflect a conserved biological strategy, observed across a broad bacterial host range and resulting in the distribution of huge phage across Earth's ecosystems.
Matheus Carnevali, P. B.*; Schulz, F.*; Castelle, C. J.*; Kantor, R. S.*; Shih, P.*; Sharon, I.*; Santini, J.*; Olm, M. R.*; 天野 由記; Thomas, B. C.*; et al.
Nature Communications (Internet), 10, p.463_1 - 463_15, 2019/01
被引用回数：35 パーセンタイル：86.04(Multidisciplinary Sciences)The metabolic platform in which microbial aerobic respiration evolved is tightly linked to the origins of Cyanobacteria (Oxyphotobacteria). Melainabacteria and Sericytochromatia, close phylogenetic neighbores to Oxyphotobacteria comprise both fermentative and aerobic representatives, or clades that are capablee of both. Here, we predict the metabolisms of Margulisbacteria from two distinct environments and Saganbacteria, and compare them to genomes of organisms from the related lineages. Melainabacteria BJ4A obtained from Mizunami site are potentially able to use O
and other terminal electron acceptors. The type C heme-copper oxygen reductase found in Melainabacteria BJ4A may be adapted to low O levels, as expected for microaerophilic or anoxic environments such as the subsurface. Notably, Melainabacteria BJ4A seems to have a branched electron transport chain, with one branch leading to a cytochrome d ubiquinol oxidoreductase and the other one leading to the type C heme-copper oxygen reductase. Both these enzymes have high affinity for O, thus are adapted to low O levels. These contemporary lineages have representatives with fermentative H-based metabolism, lineages capable of aerobic or anaerobic respiration, and lineages with both. Our findings support the idea that the ancestor of these lineages was an anaerobe in which fermentation and H metabolism were central metabolic features.
Hug, L. A.*; Baker, B. J.*; Anantharaman, K.*; Brown, C. T.*; Probst, A. J.*; Castelle, C. J.*; Butterfield, C. N.*; Hernsdorf, A. W.*; 天野 由記; 伊勢 孝太郎; et al.
Nature Microbiology (Internet), 1(5), p.16048_1 - 16048_6, 2016/05
被引用回数：1209 パーセンタイル：99.97(Microbiology)生命の系統樹は生物学において最も重要な中心テーマの一つである。遺伝子調査によると、莫大な数のブランチの存在が示唆されているが、フルスケールに近い系統樹でさえわかりにくいのが現状である。本研究では、これまでに報告されてきた配列情報に加えて、新たに取得した未培養生物のゲノム情報を用いて、バクテリア,アーキア,真核生物を含む系統樹を更新した。系統樹の描写は、全体的な概容とそれぞれの主要な系統における多様性のスナップショットの両方について行った。その結果、バクテリアの多様化の優勢性が示され、培養されていない生物種の重要性とともに主要な放射構造においてそれらの生物種の重要な進化が集中している現象が強調された。
Ghobadi, A. F.*; Letteri, R.*; Parelkar, S. S.*; Zhao, Y.; Chan-Seng, D.*; Emrick, T.*; Jayaraman, A.*
Biomacromolecules, 17(2), p.546 - 557, 2016/02
被引用回数：15 パーセンタイル：55.55(Biochemistry & Molecular Biology)We report the effect of embedding zwitterionic sulfobetaine (SB) groups in cationic comb polymers on polymer-DNA binding complexes (polyplexes), using a combination of experiments and molecular simulations. Ring-opening metathesis polymerization (ROMP) produced comb polymers with tetralysine (K4) and SB pendent groups. Dynamic light scattering, zeta potential measurements, and fluorescence-based experiments, together with coarse-grained molecular dynamics simulations, described the effect of SB groups on the size, shape, surface charge, composition, and DNA binding strength of polyplexes formed using these comb polymers. Experiments and simulations showed that increasing SB composition in the comb polymers decreased polymer-DNA binding strength, while the SB groups distributed throughout the polyplex. This allows polyplexes to maintain a positive surface charge and provide high levels of gene expression in live cells.
Raman, S.*; Nestor Jr., C. W.*; 市原 晃; Trzhaskovskaya, M. B.*
Physical Review C, 66(4), p.044312_1 - 044312_23, 2002/10
被引用回数：52 パーセンタイル：89.78(Physics, Nuclear)励起状態にある原子核が
線を放出する代わりにK,L,M,…原子軌道電子を放出する現象を、線の内部転換と呼ぶ。核構造を解析するために、内部転換が起こる確率と線が出る確率との比で定義される、内部転換係数の測定が広く行われている。現在までに5%の誤差内で測定された100種類の内部転換係数について、理論値との比較を行った。理論計算には、相対論的Harterr-Fock-Slater(RHFS)法とDirac-Fock(DF)法の2種類を用いた。その結果、RHFS法よりもDF法による理論計算の方が実験値をより良く再現することを確認した。さらに、DF計算で取り入れた(1)電子の交換相互作用,(2)原子内の電子の空孔状態,(3)有限な核半径の効果の重要性を定量的に示した。
Raman, R.*; 伊丹 潔
プラズマ・核融合学会誌, 76(10), p.1079 - 1087, 2000/10
JT-60Uへの応用を考えた、コンパクト・トロイド(CT)入射装置の概念設計についての論文である。0.4mgの重水素燃料を10Hzの周波数で、2TのJT-60Uプラズマに300km/sの速度で入射できる設計である。電源の主要部分は、CTの形成用に80個の、加速用100個のコンデンサー・バンクからなる。JT-60U入射口でのリップルトロイダル磁場及びポロイダル磁場をシールドするために、超電導金属の受動的磁気シールドを新たに考案した。
