筑波大学 特別経費プロジェクト 「生命の樹」研究機能の充実 -多様な非モデル生物研究に基づく生命原理の再構築-

発表論文(2015)

【2015】

Yamamoto T, Okuda H, Nozawa R, Furukawa J, Miura K. (2015) Enhancement of cold tolerance promotes resistance to aluminum stress. Int. J. Plant Biol. Res 3: 6.

Kigoshi Y, Fukuda T, Endo T, Hayasaka N, Iemura S, Natsume T, Tsuruta F, Chiba T. (2015) CACUL1/CAC1 Regulates the Antioxidant Response by Stabilizing Nrf2. Sci Rep 5:12857. doi: 10.1038/srep12857.

Tsuruta F, Kim J, Fukuda T, Kigoshi Y, Chiba T. (2015) The intronic region of Fbxl12 functions as an alternative promoter regulated by UV irradiation. Biochemistry and Biophysics Reports 3:100-107. doi:10.1016/j.bbrep.2015.07.010

Sheikh S, Gloeckner G, Kuwayama H, Schaap P, Urushihara H, Baldauf LS. (2015) Root of Dictyostelia based on 213 universal proteins. Molecular Phylogenetics and Evolution 92:53–62.

Komura-Kawa T, Hirota K, Shimada-Niwa Y, Yamauchi R, Shimell M, Shinoda T, Fukamizu A, O’Connor MB, Niwa R. (2015) The Drosophila zinc finger transcription factor ouija board controls ecdysteroid biosynthesis through specific regulation of spookier. PLoS Genet 11: e1005712. プレスリリース

Hirakawa Y, Ishida K. (2015) Prospective function of FtsZ proteins in the secondary plastid of chlorarachniophyte algae. BMC Plant Biol 15: 276

Hashimoto N, Kurita Y, Murakami K, Wada H. (2015) Cleavage pattern and development of isolated D blastomeres in bivalves.Journal of Experimental Zoology Part B Molecular and Developmental Evolution 324:13-21. doi:10.1002/jez.b.22585.

Suzuki DG, Murakami Y, Escriva H, Wada H. (2015) A comparative examination of neural circuit and brain patterning between the lamprey   and amphioxus reveals the evolutionary origin of the vertebrate visual center. Journal of Comparative Neurology 523:251-261. doi:10.1002/cne.23679

Suzuki DG, Murakami Y, Yamazaki Y, Wada H. (2015) Expression patterns of Eph genes in the “dual visual development” of the lamprey and their significance in the evolution of vision in vertebrates. Evolution and Development 17:139-147. doi:10.1111/ede.12119

Norio Miyamoto N, Wada H. (2015) Hemichordates: Development. In: eLS. John Wiley & Sons Ltd, Chichester. doi:10.1002/9780470015902.a0004110.pub2

Morino Y, Koga H ,Wada H. (2015) The conserved genetic background for pluteus arm development
in brittle stars and sea urchin. Evolution and Development 18:89-95. doi:10.1111/ede.12174.

Sousounis K, Qi F, Yadav MC, Millan JL, Toyama F, Chiba C, Eguchi Y, Eguchi G,Tsonis PA.
(2015) A robust transcriptional program in newts undergoing multiple events of lens regeneration. eLife 2015;4:e09594. doi:http://dx.doi.org/10.7554/eLife.09594

Kudo Y, Chiba C, Konoki K, Cho Y, Yotsu-Yamashita M. (2015) Confirmation of the absence of tetrodotoxin and its analogues in the juveniles of the Japanese fire-bellied newt, Cynops pyrrhogaster, captive-reared from eggs in the laboratory using HILIC-LC-MS. Toxicon 101:101-105.

Yamamoto T, Okuda H, Nozawa R, Furukawa J, Miura K. (2015) Enhancement of cold tolerance promotes resistance to aluminum stress. International Journal of Plant Biological Research 3(2):1032.

Noguchi F, Shimamura S, Nakayama T, Yazaki Y, Yabuki A, Hashimoto T, Inagaki Y, Fujikura K, Takishita K. Metabolic capacity of mitochondrion-related organelles in the free-living anaerobic stramenopile Cantina marsupialis. (2015) Protist 166:534-550. doi: 10.1016/j.protis.2015.08.002

Ishikawa SA, Kamikawa R, Inagaki Y. Multiple conversion between the genes encoding bacterial class-I release factors. (2015) Scientific Reports 5:12406. doi: 10.1038/srep12406

Hozumi A, Horie T, Sasakura Y. (2015) Neuronal map reveals the highly regionalized pattern of the juvenile central nervous system of the ascidian Ciona intestinalis. Developmental Dynamics 244:1375-1393.

Matsunobu S, Sasakura Y. (2015) Time course for tail regression during metamorphosis of the ascidian Ciona intestinalis. Developmental Biology 405:71-81.

Narudo Kawai, Yosuke Ogura, Tetsuro Ikuta, Hidetoshi Saiga, Mayuko Hamada, Tetsushi Sakuma, Takashi Yamamoto, Nori Satoh, Yasunori Sasakura. (2015) Hox10-regulated endodermal cell migration is essential for development of the ascidian intestine. Developmental Biology 403:43-56.

Nakano H. (2015) What is Xenoturbella? Zoological Letters 1:22. doi: 10.1186/s40851-015-0018-z

Nakano H, Kakui K, Kajihara H, Shimomura M, Jimi N, Tomioka S, Tanaka H, Yamasaki H, Tanaka M, Izumi T, Okanishi M, Yamada Y, Shinagawa H, Sato T, Tsuchiya Y, Omori A, Sekifuji M, Kohtsuka H. (2015) JAMBIO Coastal Organism Joint Surveys reveals undiscovered biodiversity around Sagami Bay. Regional Studies in Marine Science 2:77-81. doi:10.1016/j.rsma.2015.05.003

Uryu O, Ameku T, Niwa R. (2015) Recent progress in understanding the role of ecdysteroids in adult insects: Germline development and circadian clock in the fruit fly Drosophila melanogaster. Zoological Letters 1: 32

Fujikawa Y, Morisaki F, Ogura A, Morohashi K, Enya S, Niwa R, Goto S, Kojima H, Okabe T, Nagano T, Inoue H. (2015) A practical fluorogenic substrate for high-throughput screening of glutathione S-transferase inhibitors. Chemical Communications. doi:10.1039/C5CC02067K

Enya S, Daimon T, Igarashi F, Kataoka H, Uchibori M, Sezutsu H, Shinoda T, Niwa R. (2015) The silkworm glutathione S-transferase gene noppera-bo is required for ecdysteroid biosynthesis and larval development. Insect Biochem Mol Biol 61:1-7. doi: 10.1016/j.ibmb.2015.04.001.

Amemiya S, Hibino T, Nakano H, Yamaguchi M, Kuraishi R, Kiyomoto M. (2015) Development of ciliary bands in larvae of the living isocrinid sea lily Metacrinus rotundus. Acta Zoologica 96: 37-44.

Nakayama T, Nakamura A, Yokoyama A, Shiratori T, Inouye I, Ishida K. (2015) Taxonomic study of a new eustigmatophycean alga, Vacuoliviride crystalliferum gen. et sp. nov. Journal of Plant Research 128: 249-257.

Urushihara H, Kuwayama H, Fukuhara K, Itoh T, Kagoshima H, Shin-I T, Toyoda A, Ohishi K, Taniguchi T, Noguchi H, Kuroki Y, Hata T, Uchi K, Mohri K, King JS, Insall RH, Kohara Y, Fujiyama A. (2015) Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation. BMC Genomics 16:80. doi:10.1186/s12864-015-1278-x

Yubuki N, Pánek T, Yabuki A, Čepička I, Takishita K, Inagaki Y, Leander BS. (2015) Morphological identities of two different marine stramenopile environmental sequence clades: Bicosoeca kenaiensis (Hilliard 1971) and Cantina marsuplialis (Larson and Patterson, 1990) gen. nov., comb. nov. Journal of Eukaryotic Microbiology. doi: 10.1111/jeu.12207

Doi A, Kita A, Kanda Y, Uno T, Asami K, Satoh R, Nakano K, Sugiura R. (2015) Geranylgeranyltransferase Cwg2-Rho4/Rho5 module is implicated in the Pmk1 MAP kinase-mediated cell wall integrity pathway in fission yeast. Genes to Cell 20:310-323.

Shiratori T, Yokoyama A, Ishida K. (2014) Phylogeny, ultrastructure, and flagellar apparatus of a new marimonad flagellate Abollifer globosa sp. nov. (Imbricatea, Cercozoa). Protist 165:808-824.

Endo Y, Toyama F, Chiba C, Mori H, Shoji K. (2015) A memory efficient short read de novo assembly algorithm. IPSJ Transactions on Bioinformatics 8:2-8.

Kushida Y, Takaine M, Nakano K, Sugai T, Numata O. (2015) Analysis of localization of γ-tubulin during conjugation of ciliate Tetrahymena thermophila using confocal lazar-scanning microscope. Zoological Science 32:25-32.

Ohhara Y, Shimada-Niwa Y, Niwa R, Kayashima Y, Hayashi Y, Akagi K, Ueda H, Yamakawa-Kobayashi K, Kobayashi S. (2015) Autocrine regulation of ecdysone synthesis by β3-octopamine receptor in the prothoracic gland is essential for Drosophila metamorphosis. Proceedings of the National Academy of Sciences of the United States of America 112:1452-1457.

Kamikawa R, Yubuki N, Yoshida M, Taira M, Ishida K, Leander BS, Miyashita H, Hashimoto T, Mayama S, Inagaki Y. (2015) Multiple losses of photosynthesis in Nitzschia (Bachillariophyceae). Phycological Research 63:19-28.

Karaiskou A, Swalla BJ, Sasakura Y, Chambon JP. (2015) Metamorphosis in solitary ascidians. Genesis 53:34-47.

Stolfi A, Sasakura Y, Chalopin D, Satou Y, Christiaen L, Dantec C, Endo T, Naville M, Nishida H, Swalla BJ, Volff JN, Voskoboynik A, Dauga D, Lemaire P. (2015) Guidelines for the nomenclature of genetic elements in tunicate genomes. Genesis 53:1-14.

Satou Y, Hirayama K, Mita K, Fujie M, Chiba S, Yoshida R, Endo T, Sasakura Y, Inaba K, Satoh N. (2015) Sustained heterozygosity across a self-incompatibility locus in an inbred ascidian. Molecular Biology and Evolution 32:81-90.

Mi-ichi F, Miyamoto T, Takao S, Ghulam J, Hashimoto T, Hara H, Nozaki T, Yoshida H. (2015) Entamoeba mitosomes play an important role in encystation by association with cholesteryl sulfate synthesis. Proceedings of the National Academy of Sciences of the United States of America 112:E2884-90. doi:10.1073/pnas.1423718112.

Arisue N, Hashimoto T. (2015) Phylogeny and evolution of apicoplasts and apicomplexan parasites. Parasitology International 64:254–259. doi:10.1016/j.parint.2014.10.005

Kamikawa R, Tanifuji G, Ishikawa SA, Onodera NT, Ishida K, Hashimoto T, Miyashita H, Mayama S, Inagaki Y. (2015) Proposal of a Twin-arginine translocator system–mediated constraint against loss of ATP synthase genes from nonphotosynthetic plastid genomes. Molecular Biology and Evolution. doi:10.1093/molbev/msv134

Kamikawa R, Tanifuji G, Kawachi M, Miyashita H, Hashimoto T, Inagaki Y. (2015) Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. Genome Biology and Evolution 7:1133-1140. doi:10.1093/gbe/evv060

Suzuki S, Shirato S, Hirakawa Y, Ishida K. (2015) Nucleomorph genome sequences of two chlorarachniophytes, Amorphochlora amoebiformis and Lotharella
vacuolata. Genome Biology and Evolution 7:1533-45. doi:10.1093/gbe/evv096.

Santos HJ, Imai K, Makiuchi T, Tomii K, Horton P, Nozawa A, Ibrahim M, Tozawa Y, Nozaki T. (2015) A novel mitosomal β-barrel outer membrane protein in Entamoeba. Scientific Reports 5:8545. doi:10.1038/srep08545.

Picazarri K, Nakada-Tsukui K, Tsuboi K, Miyamoto E, Watanabe N, Kawakami E, Nozaki T. (2015) Atg8 is involved in endosomal and phagosomal acidification in the parasitic protist Entamoeba histolytica. Cellular Microbiology. doi:10.1111/cmi.12453

Takeshima K, Sato K, Nabekura T, Nagamune K, Hamada H, Yoshikawa H, Shibuya A, Shibuya K. (2015) Increased CD11b+ Gr-1+ cell population in the placenta after infection with Toxoplasma gondii. Microbiology and Immunology 59:95-98. doi:10.1111/1348-0421.12225.

Shoji M, Isobe H, Yamaguchi K. (2015) Full Geometry Optimizations of the CaMn4O4 Model Cluster for the Oxygen Evolving Complex of Photosystem II. Chemical Physics Letters 640:23-30. doi:10.1016/j.cplett.2015.10.006.

Shoji M, Isobe H, Yamaguchi K. (2015) QM/MM Study of the S2 to S3 Transition Reaction in the Oxygen-Evolving Complex of Photosystem II. Chemical Physics Letters 636:172-179. doi:10.1016/j.cplett.2015.07.039.

Hanaoka K, Tanaka W, Kayanuma M, Shoji M. (2015) A QM/MM study of the 5'-AMP DNA hydrolysis of aprataxin. Chemical Physics Letters 631-632:16-20. doi:10.1016/j.cplett.2015.04.053.

Harada R, Takano Y, Shigeta Y. (2015) Efficient conformational sampling of proteins based on a multi-dimensional inverse histogram: An application to folding of chignolin in explicit solvent. Chemical Physics Letters 630:68-75. doi: 10.1002/jcc.23854

Shoji M, Isobe H, Yamanaka S, Suga M, Akita F, Shen JR, Yamaguchi K. (2015) On the guiding principles for lucid understanding of the damage-free S1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II. Chemical Physics Letters 627(1):44-52. doi:10.1016/j.cplett.2015.03.033.

Nagai M, Kobayashi C, Nagai Y, Imai K, Mizusawa N, Sakurai H, Neya S, Kayanuma M, Shoji M, Nagatomo S. (2015) Involvement of Propionate Side Chains of the Heme in Circular Dichroism of Myoglobin: Experimental and Theoretical Analyses. Journal of Physical Chemistry B 119:1275-1287.

Komatsu Y, Kayanuma M, Shoji M, Yabana K, Shiraishi K, Umemura M. (2015) Light absorption and excitation energy transfer calculations in primitive photosynthetic bacteria. Molecular Physics 113:1413-1421.

Komatsu Y, Umemura M, Shoji M, Kayanuma M, Yabana K, Shiraishi K. (2015) Light absorption efficiencies of photosynthetic pigments: the dependence on spectral types of central stars. International Journal of Astrobiology 14:505-510.

Shoji M, Isobe H, Yamanaka S, Suga M, Akita F, Shen JR, Yamaguchi K. (2015) Theoretical studies of the damage-free S1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Chem. Phys. Lett. 623:1-7.

Shoji M, Isobe H, Yamanaka S, Umeda Y, Kawakami K, Kamiya N, Shen JR, Nakajima T, Yamaguchi K. (2015) Theoretical modeling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen-evolving complex of photosystem II. Molecular Physics 113:359-384.

Kayanuma M, Hanaoka K, Shoji M, Shigeta Y. (2015) A QM/MM Study of Initial Steps of Catalytic Mechanism of Nitrile Hydratase. Chemical Physics Letters 623:8-13. doi:10.1016/j.cplett.2015.01.039

Harada H, Takano Y, Shigeta Y. (2015) Enhanced Conformational Sampling Method for Proteins Based on the TaBoo SeArch (TBSA) Algorithm: Application to the Folding of a Mini-protein, Chignolin. Journal of Computational Chemistry accepted. doi:10.1002/jcc.23854

Matsui T, Kitagawa Y, Okumura M, Shigeta Y. (2015) Accurate Standard Hydrogen Electrode Potential and Applications to the Redox Potentials of Vitamin C and NAD/NADH. Journal of Physical Chemistry A 119:369-376. doi:10.1021/jp508308y

Shigeta Y, Harada H, Kayanuma M, Harada H. (2015) Quantal cumulant dynamics for real-time simulations of quantum many-body systems. International Journal of Quantum Chemistry (invited review) 115:300-308. doi: 10.1002/qua.24820

Harada H, Nakamura T, Takano Y, Shigeta Y. (2015) Protein folding pathways extracted by Outlier FLOODing method (OFLOOD) Journal of Computational Chemistry 36:97-102. doi: 10.1002/jcc.23773.