List of Publications 2018
2020 2019 2017
Hara, Y., Yamaguchi, K., Onimaru, K., Kadota, M., Koyanagi, M., Keeley, SD., Tatsumi, K., Tanaka, K., Motone, F., Kageyama, Y., Nozu, R., Adachi, N., Nishimura, O., Nakagawa, R., Tanegashima, C., Kiyatake, I., Matsumoto, R., Murakumo, K., Nishida, K., Terakita, S., Kuratani, S., Sato, K., Hyodo, S., Kuraku, S. Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. (2018) Nature Ecology and Evolution, 2, 1761-1771. doi:10.1038/s41559-018-0673-5
Shen, X.X., Opulente, D.A., Kominek, J., Zhou, X., Steenwyk, J.L., Buh, K.V., Haase, M.A.B., Wisecaver, J.H., Wang, M., Doering, D.T., Boudouris, J.T., Schneider, R.M., Langdon, Q.K., Ohkuma, M., Endoh, R., Takashima, M., Manabe, R.I,. Čadež, N., Libkind, D., Rosa, C.A., DeVirgilio, J., Hulfachor, A.B., Groenewald, M., Kurtzman, C.P., Hittinger, C.T., Rokas, A. Tempo and mode of genome evolution in the budding yeast subphylum. (2018) Cell, (available online 8 November 2018) doi: 10.1016/j.cell.2018.10.023
Nakajima, A., A. Vogelzang, M. Maruya, M. Miyajima, M. Murata, A. Son, T. Kuwahara, T. Tsuruyama, S. Yamada, M. Matsuura, H. Nakase, D.A. Peterson, S. Fagarasan, and K. Suzuki. 2018. IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J Exp Med 215:2019-2034. doi:10.1084/jem.20180427
Sergey P. Laptenok , Agnieszka A. Gil, Christopher R. Hall, Andras Lukacs, James N. Iuliano, Garth A. Jones, Gregory M. Greetham, Paul Donaldson, Atsushi Miyawaki, Peter J. Tonge, Stephen R. Meech (2018) Infrared spectroscopy reveals multi-step multi-timescale photoactivation in the photoconvertible protein archetype dronpa. Nature Chemistry 10, 845-852. doi:10.1038/s41557-018-0073-0
Otaka, J., Shimizu, T., Futamura, Y., Hashizume, D., Osada, H. Structures and synthesis of hitoyopodins: bioactive aromatic sesquiterpenoids produced by the mushroom Coprinopsis cinerea. (2018) Organic Letters, 20, 6294-6297. doi: 10.1021/acs.orglett.8b02788
Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET. Core microbiomes for sustainable agroecosystems. Nature Plants 4: 247-257. (2018) doi:10.1038/s41477-018-0139-4
Ostria-Gallardo E, Ranjan A, Ichihashi Y, Corcuera L, Sinha N. Decoding the gene co-expression network underlying the ability of Gevuina avellana to live in diverse light conditions. New Phytologist 220(1): 278-287. (2018) doi:10.1111/nph.15278
Iwano, S., Sugiyama, M., Hama, H., Watakabe, A., Hasegawa, N., Kuchimaru, T., Tanaka K.Z., Takahashi, M., Ishida, Y., Hata, J., Shimozono, S., Namiki, K., Fukano, T., Kiyama, M., Okano, H., Kizaka-Kondoh, S., McHugh T.J., Yamamori, T., Hioki, H., Maki, S., Miyawaki, A. Single-cell bioluminescence imaging of deep tissue in freely moving animals. (2018) Science, 359, 935-939. doi:10.1126/science.aaq1067
Myung, J., Schmal, C., Hong, S., Tsukizawa, Y., Rose, P., Zhang, Y., Holtzman, M.J., De Schutter, E., Herzel, H., Bordyugov, G., Takumi, T. The choroid plexus is an important circadian clock component. (2018) Nature Communications, 9, 1062. doi: 10.1038/s41467-018-03507-2.
Costea, PI., Hildebrand, F., Manimozhiyan, A., Bäckhed, F., Blaser, MJ., Bushman, FD., de Vos, WM., Ehrlich, SD., Fraser, CM., Hattori, M., Huttenhower, C., Jeffery, IB., Knights, D., Lewis, JD., Ley, RE., Ochman, H., O'Toole, PW., Quince, C., Relman, DA., Shanahan, F., Sunagawa, S., Wang, J., Weinstock, GM., Wu, GD., Zeller, G., Zhao, L., Raes, J., Knight, R., Bork, P. Enterotypes in the landscape of gut microbial community composition. (2018) Nat. Microbiol., 3, 8-16. doi: 10.1038/s41564-017-0072-8.
Takumi, T., Tamada, K. CNV biology in neurodevelopmental disorders. (2018)Current Opinion in Neurobiology, 48, 183-192. doi: 10.1016/j.conb.2017.12.004.
Suzuki S, Endo R, Manabe R, Ohkuma M, Hirakawa Y. Multiple losses of photosynthesis and convergent reductive genome evolution in the colorless green algae Prototheca. (2018) Scientific Reports, 8, 940. doi: 10.1038/s41598-017-18378-8
Kaizuka, T., Takumi, T. Postsynaptic density proteins and their involvement in neurodevelopmental disorders. (2018)Journal of Biochemistry, doi: 10.1093/jb/mvy022.
Wu, M., Takemoto, M., Luo, H., Xu, J.J., Lu, M.H., Kameyama, M., Takumi, T., Song, W.J. A novel role of the antitumor agent tricyclodecan-9-yl-xanthogenate as an open channel blocker of KCNQ1/KCNE1. (2018) European Journal of Pharmacology, doi: 10.1016/j.ejphar.2018.02.013.
Koizumi T, Hattori M, Nara K. Ectomycorrhizal fungal communities in alpine relict forests of Pinus pumila on Mt. Norikura, Japan.(2018) Mycorrhiza, 28, 129-145. doi: 10.1007/s00572-017-0817-5.
Chiou, TY., Suda, W., Oshima, K., Hattori, M., Matsuzaki, C., Yamamoto, K., Takahashi, T. Lactobacillus kosoi sp. nov., a fructophilic species isolated from kôso, a Japanese sugar-vegetable fermented beverage. (2018) Antonie Van Leeuwenhoek, in press. doi:10.1007/s10482-018-1019-7.
Kumagai, Y., Yoshizawa, S., Nakajima, Y., Watanabe, M., Fukunaga, T., Ogura, Y., Hayashi, T,, Oshima, K., Hattori, M., Ikeuchi, M., Kogure, K., DeLong, EF., Iwasaki, W. Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia. (2018) ISME J., in press. doi:10.1038/s41396-018-0058-4.
Nanki, K., Mizuno, S., Matsuoka, K., Ono, K., Sugimoto, S., Kiyohara, H., Arai, M., Nakashima, M., Takeshita, K., Saigusa, K., Senoh, M., Fukuda, T., Naganuma, M., Kato, H., Suda, W., Hattori, M., Kanai, T. Fecal microbiota transplantation for recurrent Clostridium difficile infection in a patient with ulcerative colitis.(2018) Intest. Res., 16, 142-146. doi: 10.5217/ir.2018.16.1.142
Mori, K., Nakamura, H., Kurooka, H., Miyachi, H., Tamada, K., Sugai, M., Takumi, T., Yokota, Y. Id2 determines intestinal identity through repression of the foregut transcription factor, Irx5. (2018)Molecluar and Cellular Biology, doi: 10.1128/MCB.00250-17.
Onimaru, K., Motone, F., Kiyatake, I., Nishida, K., Kuraku, S. A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum). (2018) Developmental Dynamics, accepted. doi:10.1002/dvdy.24623
Onimaru, K., Kuraku, S. Inference of the ancestral vertebrate phenotype through vestiges of the whole genome duplications. (2018) Briefings in Functional Genomics, accepted. doi: 10.1093/bfgp/ely008
Nogawa, T,. Kato, N., Shimizu, T., Okano, A., Futamura, Y., Takahashi, S., Osada, H. Wakodecalines A and B, new decaline metabolites isolated from a fungus Pyrenochaetopsis sp. RK10-F058 (2018) Journal of Antibiotics, 71, 123–128. doi: 10.1038/ja.2017.103
Kawaichi, S., Yamada, T., Umezawa, A., McGlynn, E. S., Suzuki, T., Dohme, N., Yoshida, T., Sako, Y., Matsushita, N., Hashimoto, K., Nakamura, R., Anodic and cathodic extracellular electron transfer by the filamentous bacterium Ardenticatena maritima 110S (2018) Front. Microbiol., doi: 10.3389/fmicb.2018.00068.
Iriki A, McCairn K. (2018) Brain mechanisms of tool-use that advance our knowledge beyond the border ~Neural correlates of “proto-language” in the monkey brain~, In: B Gulyás, J W Vasbinder, (Eds.), Cultural Patterns and Neurocognitive Circuits II: East-West Connections, World Sci Pub, Singapore, pp 73-111. doi: 10.1142/9789813230484_0004
Woodward A, Hashikawa T, Maeda M, Kaneko T, Hikishima K, Iriki A, Okano H, Yamaguchi Y. The Brain/MINDS digital marmoset brain atlas.(2018) Sci Data, 5,180009. doi: 10.1038/sdata.2018.9
Kato M, Yokoyama C, Kawasaki A, Takeda C, Koike T, Onoe H, Iriki A. Individual identity and affective valence in marmoset calls: in vivo brain imaging with vocal sound playback. (2018) Anim Cogn, in press. doi:10.1007/s10071-018-1169-z
Iriki A, Okano HJ, Sasaki E, Okano H. (Eds.), Hashikawa T, Hikishima K, Nakatomi R. (Contributors). The 3-Dimensional Atlas of the Marmoset Brain: Reconstructible in Stereotaxic Coordinates. (2018) Springer, Tokyo, in press. doi: 10.1007/978-4-431-56612-0
Kumazawa-Manita N, Hashikawa T, Iriki A. The 3D Stereotaxic Brain Atlas of the Degu (Octodon degu): with MRI and Histology Digital Model with a Freely Rotatable Viewer. (2018) Springer, Tokyo, in press. doi: 10.1007/978-4-431-56615-1
Kosugi A, Takemi M, Tia b, Castagnola E, Ansaldo A, Sato K, Awiszus F, Seki K, Ricci D, Fadiga L, Iriki A, Ushiba J. Accurate motor mapping using micro-electrocorticographic stimulation and stochastic threshold-hunting algorithm: a common marmoset study.(2018) J Neural Eng, in press. doi: 10.1088/1741-2552/aab307
Noda, S., Shimizu, D., Yuki, M., Kitade, O., Ohkuma, M. Host- symbiont co-speciation of termite-gut cellulolytic protist of the genera Teranympha and Eucomonympha and their Treponema endosymbionts. (2018) Microbes and Environments, 33, 26-33. doi: 10.1264/jsme2.ME17096
Utami, Y.D., Kuwahara, H., Murakami, T., Morikawa, T., Sugaya, K., Kihara, K., Yuki, M., Lo, N., Deevong, P., Hasin, S., Boonriam, W., Inoue, T., Yamada, A., Ohkuma, M., Hongoh, Y. Phylogenetic diversity and single-cell genome analysis of “Melainabacteria”, a non-photosynthetic cyanobacterial group, in the termite gut. (2018) Microbes and Environments, 33: 50-57. doi: 10.1264/jsme2.ME17137
Yuki M, Sakamoto M, Nishimura Y, Ohkuma M. Lactococcus reticulotermitis sp. nov., isolated from the gut of thesubterranean termite Reticulitermes speratus. (2018)impactInternational Journal of Systematic and Evolutionary Microbiology, 68, 596-601. 10.1099/ijsem.0.002549
Takashima M, Sriswasdi S, Manabe R, Ohkuma M, Sugita T, Iwasaki W. A Trichosporonales genome tree based on 27 haploid and three evolutionary conserved ‘natural’ hybrid genomes. (2018) Yeast, 35, 99-111. doi:10.1002/yea.3284
Wardell, CP., Fujita, M., Yamada, T., Simbolo, M., Fassan, M., Karlic, R., Polak, P., Kim, J., Hatanaka, Y., Maejima, K., Lawlor, RT., Nakanishi, Y., Mitsuhashi, T., Fujimoto, A., Furuta, M., Ruzzenente, A., Conci, S., Oosawa, A., Sasaki-Oku, A., Nakano, K., Tanaka, H., Yamamoto, Y., Kubo, M., Kawakami, Y., Aikata, H., Ueno, M., Hayami, S., Gotoh, K., Ariizumi, S., Yamamoto, M., Yamaue, H., Chayama, K., Miyano, S., Getz, G., Scarpa, A., Hirano, S., Nakamura, T., and Nakagawa, H. Genomic characterization of biliary tract cancers identifies their driver genes and predisposing mutations. (2018) J Hepatol, in press. doi: 10.1016/j.jhep.2018.01.009
Furuta, M., Tanaka, H., Shiraishi, Y., Unida, T., Imamura, M., Fujimoto, A., Fujita, M., Oku-Sasaki, A., Maejima, K., Nakano, K., Kawakami, Y., Arihiro, K., Aikata, H., Ueno, M., Hayami, S., Ariizumi, S., Yamamoto, M., Gotoh, K., Ohdan, H., Yamaue, H., Miyano, S., Chayama, K., and Nakagawa, H. Characterization of HBV integration patterns and timing in liver cancer and HBV-infected liver. (2018) Oncotarget, in press.
VanderWeele, DJ., Finney, R., Katayama, K., Gillard, M., Paner, G., Imoto, S., Yamaguchi, R., Wheeler, D., Cam, M., Pontier, A., Maejima, K., Sasaki-Oku, A., Nakano, K., Tanaka, H., Kubo, K., Ratain, MJ., Miyano, S., and Nakagawa, H. Genomic heterogeneity within individual prostate cancer foci impacts predictive biomarkers of targeted therapy. (2018) Eur Urol Focus, in press. doi:10.1016/j.euf.2018.01.006
Kanaya, T., Sakakibara, S., Jinnohara, T., Hachisuka, M., Tachibana, N., Hidano, S., Kobayashi,T., Kimura, S., Iwanaga, T., Nakagawa, T., Katsuno, T., Kato, N., Akiyama, T., Sato, T., Williams, I. R., Ohno, H. Development of intestinal M cells and follicle-associated epithelium is regulated by TRAF6-mediated NF-kB signaling. (2018) J. Exp. Med. 215:501-519.doi: 10.1084/jem.20160659.
Kato, N., Furutani, S., Otaka, J., Noguchi, A., Kinugasa, K., Kai, K., Hayashi, H., Ihara, M., Takahashi, S., Matsuda, K., Osada, H. Biosynthesis and structure-activity relationship studies of okaramines that target insect glutamate-gated chloride channels.(2018) ACS Chem. Biol.,13 (3): 561-566. doi: 10.1021/acschembio.7b00878
Takagi, H., Nogawa, T., Futamura, Y., Takahashi, S., and Osada, H. Kinanthraquinone, a new anthraquinone carboxamide isolated from Streptomyces reveromyceticus SN-593-44.(2018) J. Antibiot. in press. doi: 10.1038/s41429-017-0020-0
Date, Y. and Kikuchi, J. Application of a deep neural network to metabolomics studies and its performance in determining important variables. (2018) Anal. Chem. 90, 1805-1810. doi: 10.1021/acs.analchem.7b03795
Asakura, T., Sakata, K., Date, Y. and Kikuchi, J. Application of ensemble deep neural network to metabolomics studies. (2018) Anal. Chim. Acta. in press. doi: 10.1016/j.aca.2018.02.045
Wei, F., Sakata, K., Asakura, T., Date, Y. and Kikuchi, J. Systemic Homeostasis in Metabolome, Ionome and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem. (2018) Sci. Rep. 8, 3478. doi: 10.1038/s41598-018-20120-x
Kikuchi, J., Ito, K. and Date, Y. Environmental metabolomics with data science as investigation of ecosystem homeostasis. (2018) Progress in NMR Spectroscopy 104, 56-88. doi: 10.1016/j.pnmrs.2017.11.003
菊地淳、武部孝行 “エコインフォマティクスによる難養殖魚種の持続的生産管理構想” (2018)アグリバイオ 28, 344-347
Yamaya-Ito, H., Shimoda, Y., Hakoyama, T., Sato, S., Kaneko, T., Hossain, M.S., Shibata, S., Kawaguchi, M., Hayashi, M., Kouchi, H., Umehara, Y. Loss-of-function of ASPARTIC PEPTIDASE NODULE- INDUCED 1 (APN1) in Lotus japonicus restricts efficient nitrogen-fixing symbiosis with specific Mesorhizobium loti strains. (2018) Plant J. 93: 5-16. doi: 10.1111/tpj.13759
Germond, A., Ichimura, T., Horinouchi, T., Fujita, H., Furusawa, C., Watanabe, T.M. Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli. Communication Biology (2018) 1:85. doi:10.1038/s42003-018-0093-8
Germond, A., Ichimura, T., Chiu, L., Fujita, K., Watanabe, T.M., Fujita, H. Cell type discrimination based on image features of molecular component distribution. Scientific Reports, volume 8, Article number: 11726 (2018) doi: 10.1038/s41598-018-30276-1
Iritani S, Torii Y, Habuchi C, Sekiguchi H, Fujishiro H, Yoshida M, Go Y, Iriki A, Isoda M, Ozaki N. (2018) The neuropathological investigation of the brain of a monkey model of autism spectrum disorder with ABCA13 deletion, Int J Dev Neurosci, 71, 130-139. doi:10.1016/j.ijdevneu.2018.09.002
Iriki A (2018) On Cognitive Evolution, Inference: International Review of Science, <http://inference- review.com/article/on-cognitive-evolution>
Onimaru, K., Tatsumi, K., Shibagaki, K., Kuraku, S. A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra. (2018) Scientific Data, 5,180197. doi: 10.1038/sdata.2018.197
Tanegashima, C., Nishimura, O., Motone, F., Tatsumi, K., Kadota, M., Kuraku, S. Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei. (2018) Scientific Data, 5, 180200. doi: 10.1038/sdata.2018.200
Hara, Y., Takeuchi, M., Kageyama, Y., Tatsumi, K., Hibi, M., Kiyonari, H., Kuraku, S. Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes. (2018) BMC Biology, 16, 40. doi: 10.1186/s12915-018-0509-4
Furuta M, Tanaka H, Shiraishi Y, Unida T, Imamura M, Fujimoto A, Fujita M, Oku-Sasaki A, Maejima K, Nakano K, Kawakami Y, Arihiro K, Aikata H, Ueno M, Hayami S, Ariizumi S, Yamamoto M, Gotoh K, Ohdan H, Yamaue H, Miyano S, Chayama K*, and Nakagawa H*. Characterization of HBV integration patterns and timing in liver cancer and HBV-infected liver. Oncotarget9:25075-25088 (2018) doi: 10.18632/oncotarget.25308
Boot A, Huang MN, Ng AW, Ho SC, Lim JQ, Kawakami Y, Chayama K, Teh BT, Nakagawa H, and Rozen SG. In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. Genome Res 28: 654-665 (2018) doi:10.1101/gr.230219.117
Kato, N., Nogawa, T., Takita, R., Kinugasa, K., Kanai, M., Uchiyama, M., Osada, H., Takahashi, S. Control of the stereochemical course of [4+2] cycloaddition during trans-decalin formation by Fsa2-family enzymes. (2018) Angewandte Chemie International Edition in English, 57, 9754-9758. doi: 10.1002/anie.201805050
Qi, J., Cheng, L., Sun, Y., Hirata, Y., Ushida, N., Ma, Z., Osada, H., Nishikawa, T., Xiang, L. Identification of an asexual reproduction inducer of phytopathogenic and toxigenic Fusarium. (2018) Angewandte Chemie International Edition in English, 57, 8100-8104. doi: 10.1002/anie.201803329
Maeda, K., Ichikawa, H., Nakajima, Y., Motoyama, T., Ohsato, S., Kanamaru, K., Kobayashi, T., Nishiuchi, T., Osada, H., Kimura, M. Identification and characterization of small molecule compounds that modulate trichothecene production by Fusarium graminearum. (2018) ACS Chemical Biology, 13, 1260-1269. doi: 10.1021/acschembio.8b00044
He, D., Li, Y., Ooka, H., Go, Y. K., Jin, F., Kim, S. H., Nakamura, R. Selective electrocatalytic reduction of nitrite to dinitrogen based on decoupled proton-electron transfer. (2018) J. Am. Chem. Soc., 140, 2012-2015. doi:10.1021/jacs.7b12774
Sato K, Kadota Y, Gan P, Bino T, Uehara T, Yamaguchi K, Ichihashi Y, Maki N, Iwahori H, Suzuki T, Shigenobu S, Shirasu K. High-Quality Genome Sequence of the Root-Knot Nematode Meloidogyne arenaria Genotype A2-O. Genome Announc. 6(26): e00519-18. (2018) doi:10.1128/genomeA.00519-18
Nakata,TM, Sato M, Wakazaki M, Sato N, Kojima K, Sekine A, Nakamura S, Shikanai T, Toyooka K, Tsukaya H and Horiguchi G. Plastid translation is essential for lateral root stem cell patterning in Arabidopsis thaliana. Biology Open (2018) doi: 10.1242/bio.028175
Hamada T, Yako M, Minegishi M, Sato M, Kamei Y, Yanagawa Y, Toyooka K, Watanabe Y, Hara-Nishimura I. Stress granule formation is induced by a threshold temperature rather than a temperature difference in Arabidopsis. J Cell Sci 131, doi: 10.1242/jcs.216051
Cui Y, Cao W, He Y, Zhao Q, Wakazaki M, Zhuang X, Gao J, Zeng Y, Gao C, Ding Y, Wong H-Y, Wong W-S, Lam H-K, Wang P, Ueda T, Rojas-Pierce M, Toyooka K, Kang B-K, Jiang L. Whole cell electron tomography reveals the nature and biogenesis of vacuoles in Arabidopsis root cells. Nature Plants (in press)
Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B, Norman JM, Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V. Computer-guided design of optimal microbial consortia for immune system modulation. (2018) Elife, Apr 17; 7. pii: e30916. doi: 10.7554/eLife.30916
Kato, N., Furutani, S., Otaka, J., Noguchi, A., Kinugasa, K., Kai, K., Hayashi, H., Ihara, M., Takahashi, S., Matsuda, K., Osada, H. Biosynthesis and structure-activity relationship studies of okaramines that target insect glutamate-gated chloride channels.(2018) ACS Chem. Biol.,13 (3), 561-566, 2018. doi: 10.1021/acschembio.7b00878
Kato N., Nogawa T., Takita R., Kinugasa K., Kanai M., Uchiyama M., Osada H., Takahashi S. Control of the stereochemical course of [4+2] cycloaddition during trans-decalin formation by Fsa2-family enzymes. Angew. Chem. Int. Ed., 57, 1-6, 2018. doi: 10.1002/anie.201805050
Jang J.-P., Hwang G.J., Kwon M.C., Ryoo I.-J., Jang M., Takahashi S., Ko S.K., Osada H., Jang J.H., Ahn J.S. Pentaminomycins A and B, Hydroxyarginine-Containing Cyclic Pentapeptides from Streptomyces sp. RK88-1441. J. Nat. Prod., 81(4), 806-810, 2018. doi: 10.1021/acs.jnatprod.7b00882
Jang J.-P.,Hwang G.J., Jang M., Takahashi S., Ko S.K., Osada H., Jang J.H., Ahn J.S. Aturanosides A and B, Glycosylated Anthraquinones with Antiangiogenic Activity from a Soil-Derived Streptomyces Species. J. Nat. Prod., 81(9), 2004-2009, 2018. doi: 10.1021/acs.jnatprod.8b00307
Son S., Hong Y.S., Futamura Y., Jang M., Lee J.K., Heo K.T., Ko S.K., Lee J.S., Takahashi S., Osada H., Jang J.H., Ahn J.S. Catenulisporolides, Glycosylated Triene Macrolides from the Chemically Underexploited Actinomycete Catenulispora Species. Org Lett. in press. Oct 31. doi: 10.1021/acs.orglett.8b03160
Kitashima DY, Kobayashi T, Woodring T, Idouchi K, Doebel T, Voisin B, Adachi T, Ouchi T, Takahashi H, Nishifuji K, Kaplan DH, Clausen BE, Amagai M, Nagao K. Langerhans Cells Prevent Autoimmunity via Expansion of Keratinocyte Antigen-Specific Regulatory T Cells. EBioMedicine 27 293-303, 2017. doi:10.1016/j.ebiom.2017.12.022
Yanagiya, K., Maejima, Y., Nakat,a H., Tokuda, M., Moriuchi, R., Dohra, H., Inoue, K., Ohkuma, M., Kimbara, K., Shintani, M. Novel self-transmissible and broad-host-range plasmids exogenously captured from anaerobic granules or cow manure. (2018) Frontiers in Microbiology, 9, 2602. doi: 10.3389/fmicb.2018.02602
Tanizawa, Y., Tada, I., Kobayashi, H., Endo, A., Maeno, S., Toyoda, A., Arita, M., Nakamura, Y., Sakamoto, M., Ohkuma, M., Tohno, M. Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 3512-3517. doi: 10.1099/ijsem.0.003020
Sujarit, K., Kudo, T., Ohkuma, M., Pathom-Aree, W., Lumyong, S. Streptomyces venetus sp. nov., an actinomycete with a blue aerial mycelium. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 3333-3339. doi: 10.1099/ijsem.0.002995
Kato, S., Yuki, M., Itoh, T., Ohkuma, M. Complete genome sequence of Ferriphaselus amnicola strain OYT1, a neutrophilic, stalk-forming, iron-oxidizing bacterium. (2018) Microbiology Resource Announcements,7, e00911-18. doi: 10.1128/MRA.00911-18
Tanimura, A., Sugita, T., Endoh, R., Ohkuma, M., Kishino, S., Ogawa, J., Shima, J., Takashima, M. Lipid production via simultaneous conversion of glucose and xylose by a novel yeast, Cystobasidium iriomotense. (2018) PLoS ONE,13, e0202164. doi: 10.1371/journal.pone.0202164
Sakamoto, M., Iino, T., Yuki, M., Ohkuma, M. Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 2074-2081. doi: 10.1099/ijsem.0.002800
Kinjo, Y., Bourguignon, T., Tong, K.J., Kuwahara, H., Lim, S.J., Yoon, K.B., Shigenobu, S., Park, Y.C., Nalepa, C.A., Hongoh, Y., Ohkuma, M., Lo, N., Tokuda, G. Parallel and gradual genome erosion in the Blattabacterium endosymbionts of Mastotermes darwiniensis and Cryptocercus wood roaches. (2018) Genome Biology and Evolution, 10,1622-1630. doi: 10.1093/gbe/evy110
Sakamoto, M., Ikeyama, N., Yuki, M., Ohkuma, M. Draft Genome Sequence of Lawsonibacter asaccharolyticus JCM 32166T, a Butyrate-Producing Bacterium, Isolated from Human Feces. (2018) Genome Announcements, 6, e00563-18. doi: 10.1128/genomeA.00563-18
Noda, S., Aihara, C., Yuki, M., Ohkuma, M. Draft genome sequence of Lactococcus sp. strain NtB2 (JCM 32569T), isolated from the gut of the higher termite Nasutitermes takasagoensis. (2018) Genome Announcements, 6, e00445-18. doi: 10.1128/genomeA.00445-18
Chiba, M., Itabashi, T., Hirai, K., Sakamoto, M., Ohkuma, M., Ishige, T., Kawasaki, S. Lactobacillus metriopterae sp. nov., a novel lactic acid bacterium isolated from the gut of grasshopper Metrioptera engelhardti. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 1484-1489. doi: 10.1099/ijsem.0.002694
Penkhrue, W., Sujarit, K., Kudo, T., Ohkuma, M., Masaki, K., Aizawa, T., Pathom-Aree, W., Khanongnuch, C., Lumyong, S. Amycolatopsis oliviviridis sp. nov., a novel polylactic acid-bioplastic-degrading actinomycete isolated from paddy soil. (2018) International Journal of Systematic and Evolutionary Microbiology,68, 1448-1454. doi: 10.1099/ijsem.0.002682
Sakamoto, M.. Iino, T., Hamada, M., Ohkuma, M. Parolsenella catena gen. nov., sp. nov., isolated from human faeces. (2018) International Journal of Systematic and Evolutionary Microbiology, 68, 1165-1172. doi: 10.1099/ijsem.0.002645
Kaizuka T, Takumi T. Postsynaptic density proteins and their involvement in neurodevelopmental disorders. (2018) J Biochem. 163, 447-455. doi: 10.1093/jb/mvy022
Horder J, Petrinovic MM, Mendez MA, Bruns A, Takumi T, Spooren W, Barker GJ, Künnecke B, Murphy DG. Glutamate and GABA in autism spectrum disorder-a translational magnetic resonance spectroscopy study in man and rodent models. (2018) Transl Psychiatry. 8, 106. doi: 10.1038/s41398-018-0155-1
Jha A, Dhungel S, Takumi T. Role of selective 5-HT2c ligands on maternal separation induced ultrasonic vocalization and c-fos expression in paternal duplicated mouse pups. (2018)Open Access J Transl Med Res, 2, 73-76. doi: 10.15406/oajtmr.2018.02.00040
Nakai N, Takumi T, Nakai J, Sato M. Common Defects of Spine Dynamics and Circuit Function in Neurodevelopmental Disorders: A Systematic Review of Findings From in Vivo Optical Imaging of Mouse Models. (2018) Front Neurosci. 12, 412. doi: 10.3389/fnins.2018.00412
Nagano M, Takumi T, Suzuki H. Critical roles of serotonin-oxytocin interaction during the neonatal period in social behavior in 15q dup mice with autistic traits. (2018) Sci Rep. 8, 13675. doi: 10.1038/s41598-018-32042-9
Nakamura T, Nakajima K, Ohnishi T, Yoshikawa T, Nakanishi M, Takumi T, Tsuboi T, Kato T. Quantitative evaluation of incomplete preweaning lethality in mice by using the CRISPR/Cas9 system. (2018) Sci Rep. 8, 16025. doi: 10.1038/s41598-018-34270-5
Oita, A., Oshima, T., Tsuboi, Y., Moriya, S., Date, Y. and Kikuchi, J. Profiling physicochemical and planktonic features from discretely/continuously sampled surface water. Sci. Total Environ. (2018) 636, 12-19. doi:10.1016/j.scitotenv.2018.04.156
Mekuchi, M., Sakata, K., Asakura, T., Yamaguchi, T., Teruya, K. and Kikuchi, J. Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus). PLoS One 13, e0197256 (2018). doi:10.1371/journal.pone.0197256
Asakura, T., Sakata, K., Date, Y. and Kikuchi, J. Regional feature extraction of various fishes based on chemical and microbial variable selection using machine learning. Anal. Methods (2018) 17, 16-26. doi:10.1039/C8AY00377G
Shiokawa, Y., Date, Y. and Kikuchi, J. Application of kernel principal component analysis and machine learning computation to an exploration of metabolites strongly associated with human lifestyles. Sci. Rep. 8, 3426 (2018). doi:10.1038/s41598-018-20121-w
Ito, K., Obuchi, Y., Chikayama, E., Date, Y. and Kikuchi, J. Exploratory machine-learned theoretical chemical shifts can closely predict metabolic mixture signals. Chem. Sci. (in press). doi:10.1039/C8SC03628D
Mekuchi, M., Asakura, T. and Kikuchi, J. New aquaculture technology based on host-symbiotic co-metabolism. Marine Metagenomics (in press).
Kato, T., Yamazaki, K., Nakajima, M., Date, Y., Kikuchi, J., Hase, K., Ohno, H., Yamazaki K. Oral administration of Porphyromonas gingivalis alters the gut microbiome and serum metabolome. (2018) mSphere 3. e00460-18. doi: 10.1128/mSphere.00460-18.
Iwasawa K, Suda W, Tsunoda T, Oikawa-Kawamoto M, Umetsu S, Takayasu L, Inui A, Fujisawa T, Morita H, Sogo T, Hattori M. Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker. Sci Rep. (2018) 8, 5480. doi: 10.1038/s41598-018-23870-w
Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B, Norman JM, Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V. Computer-guided design of optimal microbial consortia for immune system modulation. Elife. (2018) 7, e30916. doi: 10.7554/eLife.30916
Kurokawa S, Kishimoto T, Mizuno S, Masaoka T, Naganuma M, Liang KC, Kitazawa M, Nakashima M, Shindo C, Suda W, Hattori M, Kanai T, Mimura M. The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study. J Affect Disord. (2018) 235, 506-512. doi: 10.1016/j.jad.2018.04.038
Nakade Y, Iwata Y, Furuichi K, Mita M, Hamase K, Konno R, Miyake T, Sakai N, Kitajima S, Toyama T, Shinozaki Y, Sagara A, Miyagawa T, Hara A, Shimizu M, Kamikawa Y, Sato K, Oshima M, Yoneda-Nakagawa S, Yamamura Y, Kaneko S, Miyamoto T, Katane M, Homma H, Morita H, Suda W, Hattori M, Wada T. Gut microbiota-derived D-serine protects against acute kidney injury. JCI Insight. (2018) 3, e97957 doi: 10.1172/jci.insight.97957
Shitashima Y, Shimozawa T, Asahi T, Miyawaki A. (2018) A dual-ligand-modulable fluorescent protein based on UnaG and calmodulin. Biochem Biophys Res Commun., 496 (3): 872-879. doi:10.1016/j.bbrc.2018.01.134
