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-




Maeno A, Kohtsuka H, Takatani K, Nakano H (2019) Microfocus X-ray CT (microCT) Imaging of Actinia equina (Cnidaria), Harmothoe sp. (Annelida), and Xenoturbella japonica (Xenacoelomorpha). Journal of Visualized Experiments in press

Nishimura Y, Shiratori T, Ishida K, Hashimoto T, Ohkuma M, Inagaki Y (2019) Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Maryophyris sp. SRT127. Scientific Reports in press

Sakamoto K, Kayanuma M, Inagaki Y, Hashimoto T, Shigeta Y (2019) In silico structural modeling and analysis of elongation factor-1alpha and elongation factor-like protein. ACS Omega in press

Yoshinari Y, Kurogi Y, Ameku T, Niwa R (2019) Endocrine regulation of female germline stem cells in the fruit fly Drosophila melanogaster. Current Opinion in Insect Science 31:14–19.

Suzaki T, Takeda N, Nishida H, Hoshino M, Ito M, Misawa F, Handa Y, Miura K, Kawaguchi M (2019) LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonius. PLoS Genetics 15: e1007865.

Sakamoto H, Hirakawa Y, Ishida K, Keeling P,J, Kita K, Matsuzaki M (2019) Puromycin selection for stable transfectants of the oyster-infecting parasite Perkinsus marinus. Parasitology International 69:13–16.

Nakano H, Miyazawa H (2019) A New Species of Orthonectida That Parasitizes Xenoturbella bocki: Implications for Studies on Xenoturbella. The Biological Bulletin 236:66-73.


Kohtsuka H, Tsuchiya Y, Nakano H (2018) First report of live Balanometra balanoides (Echinodermata: Crinoidea), with observations on its coloration, collected from the Sagami Sea. Biogeography 20:41-44.

Hirai K, Wang Z, Miura K, Hayashi T, Awasaki T, Wada M, Keira Y,  Ishikawa HO, Sawamura K (2018) Genetic Analyses of Elys Mutations in Drosophila Show Maternal-Effect Lethality and Interactions with Nucleoporin Genes. G3: Genes, Genomes, Genetics 8:7 2421-2431

Miyanaga Y, Kamimura Y, Kuwayama H,  Devreotes PN, Ueda M (2018) Some chemotactic mutants can be progress through development in chimeric populations. Biochemical and biophysical research communications 507:304-310.

Takemae H, Kobayashi K, Sugi T, Han Y, Gong H, Ishiwa A, Recuenco FC, Murakoshi F, Takano R, Murata Y, Nagamune K, Horimoto T, Akashi H, Kato K (2018) Toxoplasma gondii RON4 binds to heparan sulfate on the host cell surface. Parasitology International 67:123–130.

Shuralev EA, Shamaev ND, Mukminov MN, Nagamune K, Taniguchi Y, Saito T, Kitoh K, Arleevskaya MI, Fedotova AY, Abdulmanova DR, Aleksandrova NM, Efimova MA, Yarullin AI, Valeeva AR, Khaertynov KS, Takashima Y (2018) Toxoplasma gondii seroprevalence in goats, cats and humans in Russia. Parasitology International 67:112–114.

Andrabi SBA, Tahara M, Matsubara R, Toyama T, Aonuma H, Sakakibara H, Suematsu M, Tanabe K, Nozaki T, Nagamune K (2018) Plant hormone cytokinins control cell cycle progression and plastid replication in apicomplexan parasites. Parasitology International 67:47–58.

Taniguchi Y, Appiah-Kwarteng C, Murakami M, Fukumoto J, Nagamune K, Matsuo T, Masatani T, Kanuka H, Hoshina T, Kitoh K, Takashima Y (2018) Atypical virulence in a type III Toxoplasma gondii strain isolated in Japan. Parasitology International 67:587–592.

Sladek V , Tokiwa H, Shimano H, Shigeta Y (2018) Protein Residue Networks from Energetic and Geometric Data: Are They Identical? Journal of Chemical Theory and Computation 4:6623–6631

Hada M, Saito S, Sato R, Miyata K, Hayashi Y, Shigeta Y, Onda K (2018) Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals. Journal of Visualized Experiments 135:e57612.

Assadi MHN, Shigeta Y (2018) The effect of octahedral distortions on the electronic properties and magnetic interactions in O3 NaTMO2compounds (TM = Ti-Ni & Zr-Pd). RSC Advances 8:13842–13849.

Shoji M, Isobe H, Shigeta Y, Nakajima T, Yamaguchi K (2018) Concerted Mechanism of Water Insertion and O2 Release during the S4 to S0 Transition of the Oxygen-Evolving Complex in Photosystem II. Journal of Physical Chemistry B 122:6491–6502.

Harada R, Shigeta Y (2018) Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. Journal of Chemical Information and Modeling 58:1397–1405.

Harada R, Shigeta Y (2018) On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins. Journal of Chemical Theory and Computation 14:3332–3341.

Assadi M.H.N, Shigeta Y (2018) Dominant role of orbital splitting in determining cathode potential in O3 NaTMO2 compounds. Journal of Power Sources 388:1–4.

Terai Y, Sato R, Yumiba T, Harada R, Shimizu K, Toga T, Ishikawa-Fujiwara T, Todo T, Iwai S, Shigeta Y, Yamamoto J (2018) Coulomb and CH-φ interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities. Nucleic Acids Research 46:6761–6772.

Sato A, Kitazawa Y, Ochi T, Shoji M, Komatsu Y, Kayanuma M, Aikawa Y, Umemura M, Shigeta Y (2018) First-principles study of the formation of glycine-producing radicals from common interstellar species. Molecular Astrophysics. 10:11–19.

Sato R, Harada R, Shigeta Y (2018) The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study. Biophysics and Physicobiology 15:18-27.

Sato R, Kitoh-Nishioka H , Kamada K, Mizokuro T, Kobayashi K, Shigeta Y (2018) Does Inactive Alkyl Chain Enhance Triplet-Triplet Annihilation of 9,10-Diphenylanthracene Derivatives? Journal of Physical Chemistry C 122:5334-5340.

Shoji M, Isobe H, Shigeta Y, Nakajima T, Yamaguchi K (2018) Nonadiabatic one-electron transfer mechanism for the O–O bond formation in the oxygen-evolving complex of photosystem II. Chemical Physics Letters 698:138–146.

Yamaguchi K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Yamada S, Katouda M, Nakajima T (2018) Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II. Molecular Physics 116:717–745.

Shoji M, Isobe H, Tanaka A, Fukushima Y, Kawakami K, Umena Y, Kamiya N, Nakajima T, Yamaguchi K (2018) Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem II: Applicability of the Jahn-Teller Deformation Formula. ChemPhotoChem 2:257–270.

Zeng J, Kamiyama T, Niwa R, King-Jones K (2018) The Drosophila CCR4-NOT complex is required for cholesterol homeostasis and steroid hormone synthesis. Developmental Biology 443:10–18.

Hoshikawa K, Fujita S, Renhu N, Ezura K, Yamamoto T, Nonaka S, Ezura H, Miura K, (2018) Efficient transient protein expression in tomato cultivars and wild species using agroinfiltration-mediated high expression system. Plant Cell Reports 38:75–84.

Yamamoto T, Kashojiya S, Kamimura S, Kameyama T, Ariizumi T, Ezura H, Miura K (2018) Application and development of genome editing technologies to the Solanaceae plants. Plant Physiology and Biochemistry 131:37–46.

Ohta M, Sato A, Renhu N, Yamamoto T, Oka N, Zhu JK, Tada Y, Suzaki T, Miura K (2018) MYC-type transcription factors, MYC67 and MYC70, interact with ICE1 and negatively regulate cold tolerance in Arabidopsis. Scientific Reports 8:11622

Yamamoto T, Hoshikawa K, Ezura K, Okazawa R, Fujita S, Takaoka M, Mason HS, Ezura H, Miura K (2018) Improvement of the transient expression system for production of recombinant proteins in plants. Scientific Reports 8:4755.

Yoshimura K, Morino Y, Wada H (2018) Regeneration of the acorn worm pygochord with the implication for its convergent evolution with the notochord. Development, Growth & Differentiation 61:158 –165.

Yamakawa, S, Morino Y, Honda M, Wada H (2018) The role of retinoic acid signaling in starfish metamorphosis. EvoDevo 9:10.

Casco-Robles RM, Watanabe A, Eto K, Takeshima K, Obata S, Kinoshita T, Ariizumi, T, Nakatani K, Nakada T, Tsonis PA, Casco-Robles MM, Sakurai K, Yahata K, Maruo F, Toyama F, Chiba C (2018) Novel erythrocyte clumps revealed by an orphan gene Newtic1 in circulating blood and regenerating limbs of the adult newt. Scientific Reports 8:1–15. プレスリリース

Ishikawa K, Tanaka A, Kogame A, Watanabe T, Tagawa Y, Matsui H (2018) Usefulness of pharmacokinetic/efficacy analysis of an investigational kisspeptin analog, TAK-448, in quantitatively evaluating anti-tumor growth effect in the rat VCaP androgen-sensitive prostate cancer model. European Journal of Pharmacology 828:126–134.

Mito T, Tani H, Suzuki M, Ishikawa K, Nakada K, Hayashi JI (2018). Mito-mice∆ and mitochondrial DNA mutator mice as models of human osteoporosis caused not by aging but by hyperparathyroidism. Experimental Animals 67:509–516.

Satoh T, Iitsuka T, Shiraishi A, Hozumi A, Satake H, Sasakura Y (2018) piRNA-like small RNAs are responsible for the maternal-specific knockdown in the ascidian Ciona intestinalis Type A. Scientific Reports 8:5869.

Araie H, Nakamura H, Toney JL, Haig HA, Plancq J, Shiratori T, Leavitt PR, Seki O, Ishida K, Sawada K, Suzuki I, Shiraiwa Y (2018) Novel alkenone-producing strains of genus Isochrysis (Haptophyta) isolated from Canadian saline lakes show temperature sensitivity of alkenones and alkenoates. Organic Geochemistry 121:89–103.

Yabuki A, Ishida K (2018) An Orphan Protist Quadricilia rotundata Finally Finds Its Phylogenetic Home in Cercozoa. Journal of Eukaryotic Microbiology 65:729–732.

Tashyreva D, Prokopchuk G, Yabuki A, Kaur B, Faktorová D, Votýpka J, Kusaka C, Fujikura K, Shiratori T, Ishida K, Horák A, Lukeš J (2018) Phylogeny and Morphology of New Diplonemids from Japan. Protist 169:158–179.

Matsuo E, and Inagaki Y  (2018) Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates. PeerJ 6: e5345.

Matsuo M, Katahata A, Satoh S, Matsuzaki M, Nomura M, Ishida K, Inagaki Y, Obokata J (2018) Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer. PLoS One 13: e0200961.

Nurkanto A, Jeelani G, Yamamoto T, Naito Y, Hishiki T, Mori M, Suematsu M, Shiomi K, Hashimoto T, Nozaki T (2018) Characterization and validation of Entamoeba histolytica pantothenate kinase as a novel anti-amebic drug target. International Journal for Parasitology: Drugs and Drug Resistance 8:125–136.

Bradley A, Hashimoto T, Ono M (2018) Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis. Frontiers in Immunology 9:1444.

Harada R, Shigeta Y (2018) An Assessment of Optimal Time Scale of Conformational Resampling in Parallel Cascade Molecular Dynamics. Molecular Simulation 44:206-212.

Ameku T, Yoshinari Y, Texada MJ, Kondo S, Amezawa K, Yoshizaki G, Shimada-Niwa Y, Niwa R (2018) Midgut-derived neuropeptide F controls germline stem cell proliferation in a mating-dependent manner.  PLoS Biology 16: e2005004. プレスリリース

Horie T, Horie R, Chen K, Cao C, Nakagawa M, Kusakabe TG, Sasakura Y, Levine M (2018) Regulatory cocktail for dopaminergic neurons in a protovertebrate identified by whole-embryo single-cell transcriptomics. Genes & Development 32:1297-1302 プレスリリース

Horie R, Hazbun A, Chen K, Cao C, Levine M, Horie T (2018) Shared evolutionary origin of vertebrate neural crest and cranial placodes.
Nature 560: 223-232 プレスリリース

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.

Ichinose N, Yada T, Wada H (2018) Asymmetry in indegree and outdegree distributions of gene regulatory networks arising from dynamical robustness Physical Review E 97:062315

Miyamoto N, Wada H (2018) Hemichordate Nervous system. Oxford Research Encyclopedias of Neuroscience 10.1093/acrefore/9780190264086.013.204

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 Scientific Reports 8:940. プレスリリース

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. Scientific Reports 8:550. プレスリリース

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.  Nature Communications 9:499. プレスリリース

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. Scientific Reports 8:5239.

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 13:e0194487.

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 5:669-678

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 10:427-433.

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. Scientific Reports 8:425.

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

Sasakura Y, Hozumi A (2018) Formation of adult organs through metamorphosis in ascidians. Wiley Interdisciplinary Reviews-Developmental Biology 7:e304.

Sasakura Y (2018) Germline Transgenesis in Ciona. Advances in Experimental Medicine and Biology 1029:109-119

Sasakura Y (2018) The Enhancer Trap in Ciona. Advances in Experimental Medicine and Biology 1029:121-129.

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



発表論文  (2017)