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Items: 25

1.

Identification of Initial Colonizing Bacteria in Dental Plaques from Young Adults Using Full-Length 16S rRNA Gene Sequencing.

Ihara Y, Takeshita T, Kageyama S, Matsumi R, Asakawa M, Shibata Y, Sugiura Y, Ishikawa K, Takahashi I, Yamashita Y.

mSystems. 2019 Sep 3;4(5). pii: e00360-19. doi: 10.1128/mSystems.00360-19.

2.

Characteristics of the Salivary Microbiota in Patients With Various Digestive Tract Cancers.

Kageyama S, Takeshita T, Takeuchi K, Asakawa M, Matsumi R, Furuta M, Shibata Y, Nagai K, Ikebe M, Morita M, Masuda M, Toh Y, Kiyohara Y, Ninomiya T, Yamashita Y.

Front Microbiol. 2019 Aug 2;10:1780. doi: 10.3389/fmicb.2019.01780. eCollection 2019.

3.

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro.

Ogata K, Takeshita T, Shibata Y, Matsumi R, Kageyama S, Asakawa M, Yamashita Y.

J Oral Sci. 2019 Aug 28;61(3):418-424. doi: 10.2334/josnusd.18-0269. Epub 2019 Aug 9.

4.

Characterization of oral microbiota and acetaldehyde production.

Yokoyama S, Takeuchi K, Shibata Y, Kageyama S, Matsumi R, Takeshita T, Yamashita Y.

J Oral Microbiol. 2018 Jul 6;10(1):1492316. doi: 10.1080/20002297.2018.1492316. eCollection 2018.

5.

Genome Replication in Thermococcus kodakarensis Independent of Cdc6 and an Origin of Replication.

Gehring AM, Astling DP, Matsumi R, Burkhart BW, Kelman Z, Reeve JN, Jones KL, Santangelo TJ.

Front Microbiol. 2017 Oct 27;8:2084. doi: 10.3389/fmicb.2017.02084. eCollection 2017.

6.

Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation.

Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20485-90. doi: 10.1073/pnas.1313620110. Epub 2013 Dec 2.

7.

Identification and structure of a novel archaeal HypB for [NiFe] hydrogenase maturation.

Sasaki D, Watanabe S, Matsumi R, Shoji T, Yasukochi A, Tagashira K, Fukuda W, Kanai T, Atomi H, Imanaka T, Miki K.

J Mol Biol. 2013 May 27;425(10):1627-40. doi: 10.1016/j.jmb.2013.02.004. Epub 2013 Feb 8.

PMID:
23399544
8.

Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation.

Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K.

Structure. 2012 Dec 5;20(12):2124-37. doi: 10.1016/j.str.2012.09.018. Epub 2012 Nov 1.

9.

Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1.

Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Oct 1;68(Pt 10):1153-7. doi: 10.1107/S1744309112036421. Epub 2012 Sep 22.

10.

Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis.

Maruyama H, Shin M, Oda T, Matsumi R, Ohniwa RL, Itoh T, Shirahige K, Imanaka T, Atomi H, Yoshimura SH, Takeyasu K.

Mol Biol Cell. 2011 Feb 1;22(3):386-98. doi: 10.1091/mbc.E10-08-0668.

11.

Isoprenoid biosynthesis in Archaea--biochemical and evolutionary implications.

Matsumi R, Atomi H, Driessen AJ, van der Oost J.

Res Microbiol. 2011 Jan;162(1):39-52. doi: 10.1016/j.resmic.2010.10.003. Epub 2010 Oct 27. Review.

PMID:
21034816
12.

Formate-driven growth coupled with H(2) production.

Kim YJ, Lee HS, Kim ES, Bae SS, Lim JK, Matsumi R, Lebedinsky AV, Sokolova TG, Kozhevnikova DA, Cha SS, Kim SJ, Kwon KK, Imanaka T, Atomi H, Bonch-Osmolovskaya EA, Lee JH, Kang SG.

Nature. 2010 Sep 16;467(7313):352-5. doi: 10.1038/nature09375.

PMID:
20844539
13.

Thermococcus kodakarensis mutants deficient in di-myo-inositol phosphate use aspartate to cope with heat stress.

Borges N, Matsumi R, Imanaka T, Atomi H, Santos H.

J Bacteriol. 2010 Jan;192(1):191-7. doi: 10.1128/JB.01115-09.

14.

Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation.

Watanabe S, Arai T, Matsumi R, Atomi H, Imanaka T, Miki K.

J Mol Biol. 2009 Dec 4;394(3):448-59. doi: 10.1016/j.jmb.2009.09.030. Epub 2009 Sep 19.

PMID:
19769985
15.

Polarity in archaeal operon transcription in Thermococcus kodakaraensis.

Santangelo TJ, Cubonov√° L, Matsumi R, Atomi H, Imanaka T, Reeve JN.

J Bacteriol. 2008 Mar;190(6):2244-8. doi: 10.1128/JB.01811-07. Epub 2008 Jan 11.

16.

Crystallization and preliminary X-ray crystallographic study of [NiFe]-hydrogenase maturation factor HypE from Thermococcus kodakaraensis KOD1.

Arai T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt 9):765-7. Epub 2007 Aug 25.

17.
18.

Crystallization and preliminary X-ray crystallographic studies of the [NiFe] hydrogenase maturation proteins HypC and HypD.

Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jun 1;63(Pt 6):538-41. Epub 2007 May 31.

19.

Disruption of a sugar transporter gene cluster in a hyperthermophilic archaeon using a host-marker system based on antibiotic resistance.

Matsumi R, Manabe K, Fukui T, Atomi H, Imanaka T.

J Bacteriol. 2007 Apr;189(7):2683-91. Epub 2007 Jan 26.

20.

Atomic force microscopy dissects the hierarchy of genome architectures in eukaryote, prokaryote, and chloroplast.

Ohniwa RL, Morikawa K, Kim J, Kobori T, Hizume K, Matsumi R, Atomi H, Imanaka T, Ohta T, Wada C, Yoshimura SH, Takeyasu K.

Microsc Microanal. 2007 Feb;13(1):3-12.

PMID:
17234031
21.

Isolation and characterization of a novel poly(vinyl alcohol)-degrading bacterium, Sphingopyxis sp. PVA3.

Yamatsu A, Matsumi R, Atomi H, Imanaka T.

Appl Microbiol Biotechnol. 2006 Oct;72(4):804-11. Epub 2006 Apr 1.

PMID:
16583228
22.

Identification of the amino acid residues essential for proteolytic activity in an archaeal signal peptide peptidase.

Matsumi R, Atomi H, Imanaka T.

J Biol Chem. 2006 Apr 14;281(15):10533-9. Epub 2006 Feb 16.

24.

Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes.

Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T.

Genome Res. 2005 Mar;15(3):352-63. Epub 2005 Feb 14.

25.

Reverse gyrase is not a prerequisite for hyperthermophilic life.

Atomi H, Matsumi R, Imanaka T.

J Bacteriol. 2004 Jul;186(14):4829-33.

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