発表論文（2016）
【2016】
Shoji M, Isobe H, Nakajima T,Yamaguchi K (2016) Large-scale QM/MM calculations of the CaMn4O5 cluster in the oxygen-evolving complex of photosystem II: comparisons with EXAFS structures. Chemical Physics Letters 658:354-363.
Shoji M, Isobe H, Shen JR, Yamaguchi K (2016) Geometric and electronic structures of the synthetic Mn4CaO4 model compound mimicking the photosynthetic oxygen-evolving complex. Physical Chemistry Chemical Physics 18:11330-11340.
Sakamoto H, Suzuki S, Nagamune K, Kita K, Matsuzaki M (2016) Investigation into the Physiological Significance of the Phytohormone Abscisic Acid in Perkinsus marinus, an Oyster Parasite Harboring a Non-Photosynthetic Plastid. The Journal of Eukaryotic Microbiology 64:440-446.
Ogura Y, Sasakura Y (2016) Switching the rate and pattern of cell division for neural tube closure. Neurogenesis 3: e1235938.
Sasakura Y, Ogura Y, Treen N, Yokomori R, Park SJ, Nakai K, Saiga H, Sakuma T, Yamamoto T, Fujiwara S, Yoshida K (2016) Transcriptional regulation of a horizontally transferred gene from bacterium to chordate. Proceeding of the Royal Society B 283: pii:20161712. プレスリリース
Nishimura Y, Tanifuji G, Kamikawa R, Yabuki A, Hashimoto T, Inagaki Y (2016) Mitochondrial genome of Palpitomonas bilix: Derived genome structure and ancestral system for cytochrome c maturation. Genome Biology and Evolution 8:3090-3098.
稲垣祐司，中山卓郎 (2016) 第17章 現在も続く細胞内共生細菌のオルガネラ化. 共生微生物 （化学同人） 大野博司編 p190-201.
Nishimura Y, Amagasa T, Inagaki Y, Hashimoto T, Kitagawa H (2016) A system for supporting phylogenetic analyses over alignments of next generation sequence data. 2016 Proceedings for the 10th International Conference on Complex, Intelligent, and Software Intensive Systems (CISIS-2016) 230-237.
Templeton T, Asada M, Jiratanh M, Ishikawa SA, Tiawsirisup S, Sivakumar T, Namangala B, Takeda M, Mohkaew K, Ngamjituea S, Inoue N, Sugimoto C, Inagaki Y, Suzuki Y, Yokoyama N, Kaewthamasorn M, Kaneko O (2016) Ungulate malaria parasites Scientific Reports 6:23230.
Harada R, Inagaki Y, Shigeta Y (2016) Protein folding and evolution. 2016 Reference Module in Materials Science and Materials Engineering DOI: 10.1016/B978-0-12-803581-8.09800-3
中山卓郎，稲垣祐司 (2016) シアノバクテリアと真核藻類の細胞統合―「窒素固定オルガネラ」へ続く道？ 生物の科学 遺伝［特集：真核細胞の共生由来オルガネラ研究最前線―広がり続ける多様性と機能］70:176-180.
稲垣祐司 (2016)共生体由来オルガネラにまつわるエトセトラ．生物の科学 遺伝［特集：真核細胞の共生由来オルガネラ研究最前線―広がり続ける多様性と機能］70:156-160.
Fukagai K, Waku T, Chowdhury AM, Kubo K, Matsumoto M, Kato H, Natsume T, Tsuruta F, Chiba T, Taniguchi H, Kobayashi A (2016) USP15 stabilizes the transcription factor Nrf1 in the nucleus, promoting the proteasome gene expression. Biochemical and Biophysical Research Communications 478:363-70.
Casco-Robles MM., Islam MR, Inami W, Tanaka HV, Kunahong A,Yasumuro H, Hanzawa S, Casco-Robles RM, Toyama F, Maruo F and Chiba C (2016) Turning the fate of reprogramming cells from retinal disorder to regeneration by Pax6 in newts. Scientific Reports 6:33761.
Sato R, Harada R, Shigeta Y (2016) Theoretical analyses on a flipping mechanism of UV-induced DNA damage. Biophysics and Physicobiology 13: 311-319.
Harada R, Nakamura T, Shigeta Y (2016) A Fast Convergent Simulated Annealing Algorithm: Simulated Annealing Outlier FLOODing (SA-OFLOOD) Method. Bulletin of the Chemical Society of Japan 89:1361-1367.
Negoro S, Kawashima Y, Shibata N, Kobayashi T, Baba T, Y.-H. Lee, Kamiya K, Shigeta Y, Nagai K, Takehara I, Kato D.-I, Takeo M, Higuchi Y (2016) Mutations affecting the internal equilibrium of the 6-aminohexanoate-dimer hydrolase reaction. FEBS Letter 590:3133-3143.
Tanaka W, Shoji M, Tomoike F, Ujiie Y, Hanaoka K, Harada R, Kayanuma M, Kamiya K, Ishida T, Masui R, Kuramitsu S, Shigeta Y (2016) Molecular Mechanisms of Substrate Specificities of Uridine-Cytidine Kinase. Biophysics and Physicobiologoy 13:77-82.
Harada R, Takano Y, Shigeta Y (2016) TaBoo SeArch (TBSA) algorithm with a modified inverse histogram for reproducing biologically relevant rare-events of proteins. Journal of Chemical Theory and Computation 12:2436-2445.
Kayanuma M, Shoji M, Yoda M, Odaka M, Shigeta Y (2016) Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study. Journal of Physical Chemistry B 120:3259–3266.
Kitajima S, Miura K, Aoki W, Yamato KT, Taira T, Murakami R, Aburaya S. (2016) Transcriptiome and proteome analyses provide insight into laticifer’s defense of Euphorbia tirucalli against pests. Plant Physiology and Biochemistry 108:434-446.
Lin XL, Niu D, Hu ZL, Kim DH, Jin YH, Cai B, Liu P, Miura K, Yun DJ, Kim WY, Lin R, Jin JB (2016) An Arabidopsis SUMO E3 ligase, SIZ1, negatively regulates photomorphogenesis by promoting COP1 activity. PLoS Genetics 12, e1006016.
Tanaka HV, Ng NCY, Yu ZY, Casco-Robles MM, Maruo F, Tsonis PA, Chiba C. (2016) A developmentally regulated switch from stem cells to dedifferentiation for limb muscle regeneration in newts. Nature Communications 7:11069. プレスリリース
Endo Y, Toyama F, Chiba C, Mori H, Shoji K. (2016) Memory Efficient de novo Assembly Algorithm using Disk Streaming of K-mers. Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016). 3:266-271. ISBN:978-989-758-170-0.
Inami W, Islam MR, Nakamura K, Yoshikawa T, Yasumuro H, Casco-Robles MM, Toyama F, Maruo F, Chiba C. (2016) Expression of two classes of Pax6 transcripts in reprogramming retinal pigment epithelium cells of the adult newt. Zoological Science 33:21-30.
Ybañez RH, Leesombun A, Nishimura M, Matsubara R, Kojima M, Sakakibara H, Nagamune K, Nishikawa Y. (2016) In vitro and in vivo effects of the phytohormone inhibitor fluridone against Neospora caninum infection. Parasitology International 65:319-322.
Tahara M, Andrabi SB, Matsubara R, Aonuma H, Nagamune K. (2016) A host cell membrane microdomain is a critical factor for organelle discharge by Toxoplasma gondii. Parasitology International 65:378-388.
Ihara F, Nishimura M, Muroi Y, Mahmoud ME, Yokoyama N, Nagamune K, Nishikawa Y. (2016) Toxoplasma gondii Infection in Mice Impairs Long-Term Fear Memory Consolidation Through Dysfunction of the Cortex and Amygdala. Infection and Immunity 84:2861-2870.
松原立真, 永宗喜三郎. (2016) アピコンプレクサ生物におけるカルシウム・シグナリングと植物ホルモン. 化学療法の領域 32:117-126.
松原立真, 永宗喜三郎. (2016) アピコンプレクサ類のもつ植物様オルガネラと植物ホルモン −オルガネラ進化学から考える感染症対策 遺伝 70:99-104.
永宗喜三郎. (2016) お肉とネコの寄生虫、トキソプラズマってナニモノ？ 衛生の友 59:2.
Suzuki S, Ishida K, Hirakawa Y (2016) Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans. Genome Biology and Evolution. 8:2672-82
Niwa YS, Niwa R (2016) Ouija board: A transcription factor evolved for only one target in steroid hormone biosynthesis in the fruit fly Drosophila melanogaster. Transcription 7: 196-202.
Tsuruta F, Takebe A, Haratake K, Kanemori Y, Kim J, Endo T, Kigoshi Y, Fukuda T, Miyahara H, Ebina M, Baba T, Chiba T. (2016) SCFFbl12 Increases p21Waf1/Cip1 Expression Level through Atypical Ubiquitin Chain Synthesis. Molecular and Cellular Biology 36:2182-94. プレスリリース
Huang L, Haratake K, Miyahara H, Chiba T. (2016) Proteasome activators, PA28γ and PA200, play indispensable roles in male fertility. Scientific Reports 6:23171.
Haratake K, Sato A, Tsuruta F, Chiba T. (2016) KIAA0368-deficiency affects disassembly of 26S proteasome under oxidative stress condition. The Journal of Biochemistry 159:609-18.
Sawamura K, Sato H, Lee CY, Kamimura Y, Matsuda M. (2016) A natural population derived from species hybridization in the Drosophila ananassae species complex on Penang Island, Malaysia. Zoological Science 33:467-475.
Sawamura K. (2016) Genome-wide analysis of hybrid incompatibility in Drosophila. Advanced Techniques in Biology & Medicine 4: 1000159.
Kuwayama H, Kubohara Y. (2016) Differentiation-inducing factor 2 modulates chemotaxis via the histidine kinase DhkC-dependent pathway in Dictyostelium discoideum. FEBS Letters 590:760-76.
Okamoto M, Yamada L, Fujisaki Y, Bloomfield G, Yoshida K, Kuwayama H, Sawada H, Mori T, Urushihara H. (2016) Two HAP2-GCS1 homologs responsible for gamete interactions in the cellular slime mold with multiple mating types: Implication for common mechanisms of sexual reproduction shared by plants and protozoa and for male-female differentiation. Developmental Biology 415:6-13.
Ogura Y, Sasakura Y. (2016) Cell-cycle compensation coupled with developmental patterning. Cell Cycle 15, 2685-2686
Ogura Y, Sasakura Y. (2016) Developmental Control of Cell-Cycle Compensation Provides a Switch for Patterned Mitosis at the Onset of Chordate Neurulation. Developmental Cell 37:148-61. プレスリリース
Morino Y, Koga H, Wada H. (2016) The conserved genetic background for pluteus arm development in brittlestars and sea urchin. Evolution and Development 18:89-95.
Koga H, Fujitani H, Morino Y, Miyamoto N, Tsuchimoto J, Shibata FT, Nozawa M, Shigenobu S, Ogura A, Tachibana K, Kiyomoto M, Amemiya S, Wada H. (2016) Experimental approach reveals the role of alx1 in the evolution of the echinoderm larval skeleton. Plos One 11:e0149067.
Mohri M, Hashimoto N, Wada H. (2016) Lineage tracing of the bivalve shell field with special interest in the descendants of the 2d blastomere. Biology Letters 12:20151055
Kurita Y, Hashimoto N, Wada H. (2016) Evolution of the molluscan body plan: the case of the anterior adductor muscle in the bivalve Septifer virgatus. Biological Journal of the Linnean Society 119:420-429
Okada K, Inohaya K, Mise T, Kudo A, Takada S, Wada H. (2016) Reiterative expression of pax1 directs pharyngeal pouch segmentation in medaka (Oryzias latipes). Development 143:1800-1810. プレスリリース
Suzuki DG, Fukumoto Y, Yoshimura M, Yamazaki Y, Kosaka J, Kuratani S, Wada H. (2016) Comparative morphology and development of extra-ocular muscles in the lamprey and gnathostomes reveal the ancestral state and developmental patterns of the vertebrate head. Zoological Letters 2:10.
Fresques T, Swartz ZS, Juliano C, Morino Y, Kikuchi M, Akasaka K, Wada H, Yajima M, Wessel MG. (2016) The diversity of nanos expression in echinoderm embryos supports different mechanisms in germ cell specification. Evolution and Development 18:267-278.
Suzuki S, Hirakawa Y, Kofuji R, Sugita M, Ishida K. (2016) Plastid genome sequences of Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia reveal remarkable structural conservation among chlorarachniophyte species. Journal of Plant Research 129:581-590.
Ameku T, Niwa R. (2016) Mating-Induced Increase in Germline Stem Cells via the Neuroendocrine System in Female Drosophila. PLOS Genetics 12:e1006123. プレスリリース
Niwa YS, Niwa R. (2016) Transcriptional regulation of insect steroid hormone biosynthesis and its role in controlling timing of molting and metamorphosis. Development, Growth & Differentiation 58:94-105.