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-




Horie R, Hazbun A, Chen K, Cao C, Levine M, Horie T* (2018)
Shared evolutionary origin of vertebrate neural crest and cranial placodes.
Nature in press DOI: 10.1038/s41586-018-0385-7

Uryu O*, Ou Q*, Komura-Kawa T, Kamiyama T, Iga M, Syrzycka M, Hirota K, Kataoka H, Honda BM, King-Jones K, Niwa R (2018)
Cooperative Control of Ecdysone Biosynthesis in Drosophila by Transcription Factors Séance, Ouija board, and Molting Defective.
Genetics 208: 605-622.
(Journal Cover: http://www.genetics.org/content/208/2.cover-expansion)

Niwa R, Nishimura T (2018)
Assembly of insect hormone enthusiasts at Nasu Highland, Japan: Report of the 3rd International Insect Hormone (21st Ecdysone) Workshop.
Genes to Cells 23: 16-21.

Miyamoto N, Wada H(2018)
Hemichordate Nervous system
Oxford Research Encyclopedias of Neuroscience

Endo M*,  Hirose M*, Honda M, Koga H, Morino Y, Kiyomoto M, Wada H (2018)
Hidden genetic history of the Japanese sand dollar Peronella (Echinoidea: Laganidae) revealed by nuclear intron sequences
Gene  659:37–43

Suzuki, S, Endoh, R, Manabe, RI, Ohkuma, M, and Hirakawa Y (2018)
Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca
Sci. Rep 8(1), 940.

Mori, K., Renhu, N., Naito, M., Nakamura, A., Shiba, H., Yamamoto, T., Suzaki, T., Iida, H., Miura, K (2018)
Ca2+-permeable mechanosensitive channels MCA1 and MCA2 mediate cold-induced cytosolic Ca2+ increase and cold tolerance in Arabidopsis.
Sci. Rep 8, 550

Nishida, H., Tanaka, S., Handa, Y., Ito, M., Sakamoto, Y., Matsunaga, S., Betsuyaku, S., Miura, K., Soyano, T., Kawaguchi, M., Suzaki, T (2018)
A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicas.
Nat. Comm 9, 499.

Záhonová K, Petrželková R, Valach M, Yazaki E, Tikhonenkov DV, Butenko A, Janouškovec J, Hrdá Š, Klimeš V, Burger G, Inagaki Y, Keeling PJ, Hampl V,  Flegontov P, Yurchenko V, Eliáš M (2018)
Extensive molecular tinkering in the evolution of the membrane attachment mechanisms of the Rheb GTPase
Sci. Rep in press

Tanifuji G, Takabayashi S, Kume K, Takagi M, Nakayama T, Kamikawa R, Inagaki Y, Hashimoto T (2018)
The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites.
PLOS one in press

Kamikawa R, Yazaki E, Tahara M, Sakura T, Matsuo E, Nagamune K, Hashimoto T, Inagaki Y (2018)
Fates of evolutionarily distinct, plastid-type glyceraldehyde 3-phosphate dehydrogenase genes in kareniacean dinoflagellates
Journal of Eukaryotic Microbiology in press

Brown MB, Heiss A, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida K, Hashimoto T, Simpson AGB, Roger AJ (2018)
Phylogenomics places orphan protistan lineages in a novel candidate super-group
Genome Biology and Evolution 10(2):427-433

Tani H, Ohnishi S, Shitara H, Mito T, Yamaguchi M, Yonekawa H, Hashizume O, Ishikawa K, Nakada K, Hayashi JI (2018)
Mice deficient in the Shmt2 gene have mitochondrial respiration defects and are embryonic lethal.
Sci Rep. 11;8(1):425.

Okajima T, Tsuruta F (2018)
Microglial dynamics during brain development
Neural Regen. Res 13(2):222-223 (invited review)

Sasakura Y, Hozumi A (2018)
Formation of adult organs through metamorphosis in ascidians
Wiley Interdiscip Rev Dev Biol, 7, e304

Miyazawa H and Nakano H (2018)
Multiple surveys employing a new sample-processing protocol reveal the genetic diversity of placozoans in Japan.
Ecology and Evolution 8: 2407-2417


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(4):439-451, 2017-07
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(6):999-1012, 2017-06

Nakano H, Miyazawa H, Maeno A, Shiroishi T, Kakui K, Koyanagi R, Kanda M, Satoh N, Omori A & Kohtsuka H (2017)
A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella.
BMC Evolutionary Biology 17: 245

Matsuo E, Inagaki Y (2017)
Trends in reconstruction of three nucleus-encoded, plastid-localized pathways for the heme, chlorophyll a and isopentenyl diphosphate biosyntheses in two separate dinoflagellate lineages bearing non-canonical plastids. PeerJ Preprints 5:e3488v1.

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.
Biochem Biophys Res Commun. 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
Biochem Biophys Res Commun. 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 doi:10.1038/s41559-017-0351-z

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.
Proc Natl Acad Sci U S A 114:E6352-6360 * equal contribution

Ichinose N, Yada T and Wada H (2017) Estimating Optimal Sparseness of Developmental Gene Networks Using a Semi-quantitative Model
Plos One12, e0176492

Hirakawa Y, Nakayama T, Keilert N, Ishida K (2017) Evolution of UhpC-type hexose-phosphate transporters in dinoflagellates.
Phycological Research 65(2):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. J Biochem 162(2):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
J Eukaryot Microbiol 64(3):293-307.

Ogura Y, Sasakura Y (2017) Emerging mechanisms regulating mitotic synchrony during animal embryogenesis.
Dev Growth Differ Epub ahead of print

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 26;12(6):e0180227.

Sasakura Y, Yoshida K, Treen N (2017) Genome Editing of the Ascidian Ciona intestinalis with TALE Nuclease.
Methods Mol Biol 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(9):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.
Dev Biol 423(2):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 5.2: 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 accepted

R. Harada, Y. Shigeta (2017) An Assessment of Optimal Time Scale of Conformational Resampling in Parallel Cascade Molecular Dynamics. Molecular Simulation accepted

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. accepted

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 accepted

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. Nat. Hist. Hum. Hist., Ser. A 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 in press

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 12;92(1):35-42.

Tsuruta F, Okajima T, Yano S, Chiba T (2017) Quantification of Endosome and Lysosome Motilities in Cultured Neurons Using Fluorescent Probes. J Vis Exp May 22;(123). doi: 10.3791/55488.

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

Ameku T, Yoshinari Y, Fukuda R, Niwa R (2017) Ovarian ecdysteroid biosynthesis and female germline stem cells. Fly doi: 10.1080/19336934.2017.1291472

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. Biochem Biophys Res Commun 482(4):863-869