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-



Del Campo, J James ER, Hirakawa Y, Fiorito R, Kolisko M, Irwin NAT, Mathur V, Boscaro V, Hehenberger E, Karnkowska A, Scheffrahn RH, Keeling PJ (2017) Pseudotrichonympha leei, Pseudotrichonympha lifesoni, and Pseudotrichonympha pearti, new species of parabasalian flagellates and the description of a rotating subcellular structure. Scientific Reports 7:16349

Nakano H, Miyazawa H, Maeno A, Shiroishi T, Kakui K, Koyanagi R, Kanda M, Satoh N, Omori A, and Kohtsuka H (2017) A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella. BMC Evolutionary Biology 17:1–11. プレスリリース

Shiratori T, Takur R, Ishida K (2017) Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a poorly studied phagotrophic biflagellate is the first characterized member of stramenopile environmental clade MAST-6. Protist 168:439-451.

Shiratori T, Fujita S, Shimizu T, Nakayama T, Ishida K (2017) Viridiuvalis adhaerens gen. et sp. nov., a novel colony-forming chlorarachniophyte.
Journal of Plant Resarch 130:999-1012

Nakayama T, Inagaki Y (2017) Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.
Scientific Reports 7:13075.

Tanifuji G, Curtis BA,Cenci U, David V, Dean S, Fiala I, Flegontov P, Johnson-MacKinnon J, Kelly S, McPhee M, Moog D, Nakayama T, Tanifuji-Onodera N, Sibbald S, Inagaki Y, Hashimoto T, Gull K, Lukeš J, Archibald JM (2017) Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Scientific Reports 7:111688.

Kamikawa R, Moog D, Zauner S, Tanifuji G, Ishida K, Miyashita H, Mayama S, Hashimoto T, Maier UG, Archibald JA, Inagaki Y (2017)
A non-photosynthetic diatom reveals early steps of reductive evolution in plastids. Molecular Biology and Evolution 34(9):2355-2366.

Shimizu A, Tani H, Takibuchi G, Ishikawa K, Sakurazawa R, Inoue T, Hashimoto T, Nakada K, Takenaga K, Hayashi JI (2017)
Cytoplasmic transfer of heritable elements other than mtDNA from SAMP1 mice into mouse tumor cells suppresses their ability to form tumors in C57BL6 mice. Biochemical and Biophysical Research Communications 2493:252-257

Kim J, Tsuruta F, Okajima T, Yano S, Sato B, Chiba T (2017)
KLHL7 promotes TUT1 ubiquitination associated with nucleolar integrity: Implications for retinitis pigmentosa.
Biochemical and Biophysical Research Communications 494: 220-226

Enya S*, Yamamoto C*, Mizuno H, Esaki T, Lin H-K, Iga M, Morohashi K, Hirano T, Kataoka H, Masujima H, Shimada-Niwa Y, Niwa R (2017)
Dual Roles of Glutathione in Ecdysone Biosynthesis and Antioxidant Function During the Larval Development in Drosophila.
Genetics 207:1519-1532. *equal contribution

Morino Y, Hashimoto N,  Wada H (2017) Expansion of TALE homeobox genes and the evolution of spiralian development.
Nature Ecology & Evolution 1:1942-1949. プレスリリース

Li Y*, Zhao D*,  Horie T*, Chen G*, Bao H, Chen S, Liu W, Horie R, Liang T, Dong B, Feng Q, Tao Q, Liu X (2017) Conserved gene regulatory module specifies lateral neural borders across bilaterians.
Proceedings of the National Academy of Sciences of the United States of America 114:E6352-6360 *equal contribution プレスリリース

Ichinose N, Yada T and Wada H (2017) Estimating Optimal Sparseness of Developmental Gene Networks Using a Semi-quantitative Model
Plos One 12: e0176492

Hirakawa Y, Nakayama T, Keilert N, Ishida K (2017) Evolution of UhpC-type hexose-phosphate transporters in dinoflagellates.
Phycological Research 65:166-170.

Morita R, Takaine M, Numata O, Nakano K (2017) Molecular dissection of the actin-binding ability of the fission yeast α-actinin, Ain1, in vitro and in vivo. The Journal of Biochemistry 162:93-102.

Kushida Y, Takaine M, Nakano K, Sugai T, Vasudevan KK, Guha M, Jiang YY, Gaertig J, Numata O (2017)
Kinesin-14 is Important for Chromosome Segregation During Mitosis and Meiosis in the Ciliate Tetrahymena thermophila
Journal of Eukaryotic Microbiology 64:293-307.

Ogura Y, Sasakura Y (2017) Emerging mechanisms regulating mitotic synchrony during animal embryogenesis.
Development, Growth & Differentiaion 9:565-579.

Osugi T, Sasakura Y, Satake H (2017) The nervous system of the adult ascidian Ciona intestinalis Type A (Ciona robusta): Insights from transgenic animal models. PLoS One 12:e0180227.

Sasakura Y, Yoshida K, Treen N (2017) Genome Editing of the Ascidian Ciona intestinalis with TALE Nuclease. Methods in Molecular Biology 1630:235-245.

Yoshida K, Nakahata A, Treen N, Sakuma T, Yamamoto T, Sasakura Y (2017) Hox-mediated endodermal identity patterns pharyngeal muscle formation in the chordate pharynx. Development 144:1629-1634.

Yoshida K, Hozumi A, Treen N, Sakuma T, Yamamoto T, Shirae-Kurabayashi M, Sasakura Y (2017)Germ cell regeneration-mediated, enhanced mutagenesis in the ascidian Ciona intestinalis reveals flexible germ cell formation from different somatic cells. Developmental Biology 423:111-125.

Kudo Y, Chiba C, Konoki K, Cho Y, Yotsu-Yamashita M (2017) Dietary administration of tetrodotoxin and its putative biosynthetic intermediates to the captive-reared non-toxic Japanese fire-bellied newt, Cynops pyrrhogaster. Toxicon 137:78-82.

Yasumuro H, Sakurai K, Toyama F, Maruo F. and Chiba C (2017) Implications of a multi-step trigger of retinal regeneration in the adult newt.
Biomedicines 5:25.

Kubohara Y, Kikuchi H, Nguyen VH, Kuwayama H, and Oshima Y (2017) Evidence that differentiation-inducing factor-1 controls chemotaxis and cell differentiation, at least in part, via mitochondria in Dictyostelium discoideum. Biology Open 6:741-751.

R. Harada, Y. Shigeta (2017) Temperature-Exchanged Parallel Cascade Selection Molecular Dynamics Accelerates Structural Transitions of Proteins. Journal of Computational Chemistry 38:2671-2674.

R. Harada, Y. Shigeta (2017) Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events. Bulletin of the Chemical Society of Japan 90:1236-1243.

Y. Shigeta, R. Harada, R. Sato, H. Kitoh-Nishioka, T. K. M. Bui, A. Sato, A. Kyan, Y. Ishii, M. Kimatsuka, S. Yamasaki, M. Kayanuma, M. Shoji (2017) Classical Cumulant Dynamics for Statistical Chemical Physics. Molecular Simulation 43:1260-1268.

R. Harada, Y. Shigeta (2017) Structural Dissimilarity Sampling with Dynamically Self-Guiding Selection. Journal of Computational Chemistry 38: 1921-1929.

Y. Ujiie, W. Tanaka, K. Hanaoka, R. Harada, M. Kayanuma, M. Shoji, T. Murakawa, T. Ishida, Y. Shigeta, H. Hayashi (2017) Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations. Journal of Physical Chemistry B 121:5536-5543.

J. Fujita, R. Harada, Y. Maeda, Y. Saito, E. Mizohata, T. Inoue, Y. Shigeta, H. Matsumura (2017)  Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus. Journal of Structural Biology 198:65-73.

R. Harada, Y. Shigeta (2017) How does the number of initial structures affect the conformational sampling efficiency and quality in Parallel Cascade Selection Molecular Dynamics (PaCS-MD)? Chemistry Letters 46:862-865.

R. Harada, Y. Shigeta (2017) Efficient conformational search based on Structural Dissimilarity Sampling: Applications to reproductions of structural transitions on Maltodextrin Binding Protein. Journal of Chemical Theory and Computation 13:1411-1423.

R. Harada, Y. Takano, Y. Shigeta (2017) Common folding processes of mini proteins: Partial formations of secondary structures initiate the immediate protein folding. Journal of Computational Chemistry 38:790-797.

M. Shoji, H. Isobe, T. Nakajima, Y. Shigeta, M. Suga, F. Akita, J.-R. Shen, K. Yamaguchi (2017) Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures. Faraday Discussions 198:83-106.

Kakui K, Suzuki A, Nakano H, Kohtsuka H (2017) Habitat of a tanaidacean Apseudes nipponicus Shiino, 1937. Bull. Kitakyushu Mus. Bulletin of Kitakyushu Museum of Natural History and Human History,Series A (Natural History) 15:1-3.

Imura E, Yoshinari Y, Niwa YS, Niwa R (2017) Protocols for Visualizing Steroidogenic Organs and Their Interactive Organs with Immunostaining in the Fruit Fly Drosophila melanogaster. Journal of Visualized Experiments 122:e55519.

Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, Cepicka I, Silberman JD, Andersson JO, Xu F, Yabuki A, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T, Roger AJ (2017) Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes.  Nature Ecology & Evolution 1:0092.

Yazaki Y, Ishikawa SA, Kume K, Kumagai A, Kamaishi T, Tanifuji G, Hashimoto T, Inagaki Y (2017) Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including parasitic species for better understanding transitions from a free-living to a parasitic lifestyle. Genes & Genetic Systems 92:35-42.

Tsuruta F, Okajima T, Yano S, Chiba T (2017) Quantification of Endosome and Lysosome Motilities in Cultured Neurons Using Fluorescent Probes. Journal of Visualized Experiments 123:e55488.

Hirakawa Y. Nakayama T, Keilert N, Ishida K (2017) Evolution of UhpC-type hexose-phosphate transporters in dinoflagellates. Phycological Research 65:166-170.

Ameku T, Yoshinari Y, Fukuda R, Niwa R (2017) Ovarian ecdysteroid biosynthesis and female germline stem cells. Fly 11:185-193.

Fukuda T, Kigoshi-Tansho Y, Naganuma T, Kazaana A, Okajima T, Tsuruta F, Chiba T (2017) CACUL1/CAC1 attenuates p53 activity through PML post-translational modification. Biochemical and Biophysical Research Communications 482:863-869.

Kuwayama H, Kikuchi H, Oshima Y, Kubohara Y (2017) Glutathione S-transferase 4 is a putative DIF-binding protein that regulates the size of fruiting bodies in Dictyostelium discoideumBiochemistry and Biophysics Reports 8:219-226.