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(2014)

【2014】

Moehninsi, Miura K, Yamada K, Shigemori H (2014) Raphanusanin-mediated resistance to pathogens is light dependent in radish and Arabidosis thaliana. Planta 240: 513-524.

Pitaksaringkarn W, Matsuoka K, Asahina M, Miura K, Sage-Ono K, Ono M, Yokoyama R, Nishitani K, Ishii T, Iwai H, & Satoh S. (2014) XTH20 and XTH19 regulated by ANAC071 under auxin flow are involved in cell proliferation in incised Arabidopsis inflorescence stems. Plant J. 80: 604-614.

Nakano H. (2014) Survey of the Japanese Coast Reveals Abundant Placozoan Populations in the Northern Pacific Ocean. Scientific Reports 4: 5356

Shirata M, Araye Q, Maehara K, Enya S, Takano-Shimizu T, Sawamura K. (2014) Allelic asymmetry of the Lethal hybrid rescue (Lhr) gene expression in the hybrid between Drosophila melanogaster and D. simulans: confirmation by using genetic variations of D. melanogaster. Genetica 142:43-48.

Sawamura K, Maehara K, Keira Y, Ishikawa HO, Sasamura T, Yamakawa T, Matsuno K. (2014) A test of double interspecific introgression of nucleoporin genes in Drosophila. G3. Genes Genomes Genetics 4:2101-2106.

Casco-Robles MM, Miura T, Chiba C. (2014) The newt (Cynops pyrrhogaster) RPE65 promoter: molecular cloning, characterization and functional analysis. Transgenic Research Published online: doi:10.1007/s11248-014-9857-1.

Nakamura K, Islam MR, Takayanagi M, Yasumuro H, Inami W, Kunahong A, Casco-Robles RM, Toyama F, Chiba C. (2014) A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster. PLoS ONE 9:e109831.

Islam MR, Nakamura K, Casco-Robles MM, Kunahong A, Inami W, Toyama F, Maruo F, Chiba C. (2014) The newt reprograms mature RPE cells into a unique multipotent state for retinal regeneration. Scientific Reports 4:6043.

Endo Y, Toyama F, Chiba C, Mori H, Shoji K. (2014) De novo short read assembly algorithm with low memory usage. Proceeding of the International Conference on Bioinformatics Models, Methods and Algorithms. 215-220. doi:10.5220/0004881002150220.

Chiba C. (2014) The retinal pigment epithelium: An important player of retinal disorders and regeneration. Experimental Eye Research 123:107-114.

Takaine M, Imada K, Numata O, Nakamura T, Nakano K. (2014) The meiosis-specific nuclear passenger protein is required for proper assembly of forespore membrane in fission yeast. Journal of Cell Science 127:4429-4442.

Takaine M, Numata O, Nakano K. (2014) Fission yeast IQGAP maintains F-actin-independent localization of myosin-II in the contractile ring. Genes to Cells 19:161-176.

Kamiya C, Ohta N, Ogura Y, Yoshida K, Horie T, Kusakabe TG, Satake H, Sasakura Y. (2014) Nonreproductive role of gonadotropin-releasing hormone in the control of ascidian metamorphosis. Developmental Dynamics. 243:1524-1535.

Niwa YS, Niwa R. (2014) Serotonergic neurons respond to nutrients and regulate the timing of steroid hormone biosynthesis in Drosophila. Nature Communications. 5:5778.

Enya S, Ameku T, Igarashi F, Iga M, Kataoka H, Shinoda T, Niwa R. (2014) A Halloween gene noppera-bo encodes a glutathione S-transferase essential for ecdysteroid biosynthesis via regulating the behaviour of cholesterol in Drosophila. Scientific Reports 4:6586.

Niwa R, Niwa YS. (2014) Enzymes for ecdysteroid biosynthesis: their biological functions in insects and beyond. (2014) Bioscience Biotechnology and Biochemistry 78:1283-1292.

Danielsen ET, Moeller ME, Dorry E, Komura-Kawa T, Fujimoto Y, Troelsen JT, Herder R, O'Connor MB, Niwa R, Rewitz KF. (2014) Transcriptional control of steroid biosynthesis genes in the Drosophila prothoracic gland by ventral veins lacking and knirps. PLoS Genetics 10:e1004343.

Niwa YS, Niwa R. (2014) Neural control of steroid hormone biosynthesis during development in the fruit fly Drosophila melanogaster. Genes and Genetic Systems 89:27-34.

Sasaki H, Yoshida K, Hozumi A, Sasakura Y. (2014) CRISPR/Cas9-mediated gene knockout in the ascidian Ciona intestinalis. Development Growth and Differentiation 56:499-510.

Iitsuka T, Mita K, Hozumi A, Hamada M, Satoh N, Sasakura Y. (2014) Transposon-mediated targeted and specific knockdown of maternally expressed transcripts in the ascidian Ciona intestinalis. Scientific Reports 4:5050.

Yoshida K, Treen N, Hozumi A, Sakuma T, Yamamoto T, Sasakura Y. (2014) Germ cell mutations of the ascidian Ciona intestinalis with TALE nucleases. Genesis 52:431-439.

Sasakura Y. (2014) Germline transformation in the ascidian Ciona intestinalis. Sexual reproduction in animals and plants (eds H. Sawada, N. Inoue, M. Iwano). Springer.

Nicholas Treen, 吉田慶太、佐々木陽香、笹倉靖徳 (2014) ホヤにおけるTALENを用いた遺伝子改変. 実験医学別冊 今すぐ始めるゲノム編集(山本卓編)pp161-168.

Treen N, Yoshida K, Sakuma T, Sasaki H, Kawai N, Yamamoto T, Sasakura Y. (2014) Tissue-specific and ubiquitous gene knockouts by TALEN electroporation provide new approaches to investigating gene function in Ciona. Development 141:481-487

Nomura M, Nakayama T, Ishida K. (2014) Detailed Process of Shell Construction in the Photosynthetic Testate Amoeba Paulinella chromatophora (Euglyphid, Rhizaria). Journal of Eukaryotic Microbiology 61:317-321.

Owari A, Hayashi A, Ishida K. (2014) Subcellular localization of minicircle DNA in the dinoflagellate Amphidinium massartii. Phycological Research 62:1-8.

Fukuda S, Iwamoto K, Atsumi M, Yokoyama A, Nakayama T, Ishida K, Inouye I, Shiraiwa Y. (2014) Screening of microalgae and aquatic plants that can eliminate radioactive cesium, iodine and strontium by bioaccumulation from radio-contaminated aquatic environment. Journal of Plant Research 127:79-89.

Hirakawa Y. (2014) Complex plastids of chlorarachniophyte algae. Perspectives in Phycology 1: 87-92.

Hirakawa Y, Ishida K. (2014) Polyploidy of endosymbiotically derived genomes in complex algae. Genome Biology and Evolution 6: 974-980

Hirakawa Y, Suzuki S, Archibald JM, Keeling PJ, Ishida K. (2014). Overexpression of molecular chaperone genes in nucleomorph genomes. Molecular Biology and Evolution 31:1437-1443

Burki F, Imanian B, Hehenberger E, Hirakawa Y, Maruyama S, Keeling PJ. (2014). Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates. Eukaryotic Cell 13: 246-255

Kuwayama H, Tohyama T, Urushihara H. (2014) Cross-species functional complementation of cellulose synthase during the development of cellular slime molds. Development Growth and Differentiation 56:526–533.

Nakayama T, Inagaki Y. (2014) Unique genome evolution in an intracellular N2-fixing symbiont of a rhopalodiacean diatom. Acta Societatis Botanicorum Poloniae 83:409-413.

Nakayama T, Kamiawa R, Tanifuji G, Kashiyama Y, Ohkouchi N, Archibald JM, Inagaki Y. (2014) Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intercellular lifestyle. Proceedings of the National Academy of Sciences of the United States of America 111:11407-11412.

Kamikawa R, Inagaki Y, Hashimoto T. (2014) Secondary loss of a cis-spliced intron after the diversification of Giardia intestinalis assemblages. BMC Research Notes 7:413.

Nishimura Y, Kamikawa R, Hashimoto T, Inagaki Y. (2014) An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333. Mobile Genetic Elements 4:e29384.

Yabuki A, Kamikawa R, Ishikawa SA, Kolisko M, Kim E, Tanabe AS, Kume K, Ishida K, Inagaki Y. (2014) Palpitomonas bilix represents a basal cryptist lineage: Insight into the character evolution in Cryptista. Scientific Reports 4:4641.

Kamikawa R, Kolisko M, Nishimura Y, Yabuki A, Brown MW, Ishikawa SA, Ishida K, Roger AJ, Hashimoto T, Inagaki Y. (2014) Gene content evolution in discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biology and Evolution 6:306-315.

石川奏太, 中尾昌広, 稲垣祐司, 橋本哲男, 佐藤三久. (2014) Non-homogeneous置換モデルに基づく進化系統樹推測のMPI/OpenMP HYBRID並列化:大規模計算システム向けプログラムの開発と性能評価. ハイパフォーマンスコンピューティングと計算科学シンポジウム(HPCS2014)論文集,情報処理学会 10-20.

Yabuki A, Kamikawa R, Ishikawa SA, Kolisko M, Kim E, Tanabe AS, Kume K, Ishida K, Inagaki Y. (2014) Palpitomonas bilix represents a basal cryptist lineage: Insight into the character evolution in Cryptista. Scientific Reports 4:4641. doi:10.1038/srep04641

Shoji M, Hanaoka K, Ujiie Y, Tanaka W, Kondo D, Umeda H, Kamoshida Y, Kayanuma M, Kamiya K, Shiraishi K, Machida Y, Murakawa T, Hayashi H. (2014) A QM/MM Study of the l-Threonine Formation Reaction of Threonine Synthase: Implications into the Mechanism of the Reaction Specificity. Journal of the American Chemical Society 136:4525-4533. doi:10.1021/ja408780c

Hanaoka K, Shoji M, Kondo D, Sato A, Yang MY, Kamiya K, Shiraishi K. (2014) Substrate mediated proton relay mechanism for the religation reaction in topoisomerase II. Journal of Biomolecular Structure & Dynamics 32:1759-1765. doi:10.1080/07391102.2013.834848.

Shoji M, Hanaoka K, Kondo D, Sato A, Umedab H, Kamiyaa K, Shiraishi K. (2014) A QM/MM study of nitric oxide reductase-catalyzed N2O formation. Molecular Physics 112:393-397. doi:10.1080/00268976.2013.830200

Marumo K, Nakada-Tsukui K, Tomii K, Nozaki T. (2014) Ligand heterogeneity of the cysteine protease binding protein family in the parasitic protist Entamoeba histolytica. International Journal for Parasitology 44:625-35. doi:10.1016/j.ijpara.2014.04.008.

Jeelani G, Nozaki T. (2014) Metabolomic analysis of Entamoeba: applications and implications. Current Opinion in Microbiology 20C:118-124. doi:10.1016/j.mib.2014.05.016.

Kawahara F, Zhang G, Suzuki T, Iwata A, Nagamune K, Nunoya T. (2014) Characterization of Eimeria brunetti isolated from a poultry farm in Japan. The Journal of Veterinary Medical Science 76:25-29. doi:10.1292/jvms.13-0239

Matsuo K, Kamai R, Uetsu H, Goto H, Takashima Y, Nagamune K. (2014) Seroprevalence of Toxoplasma gondii infection in cattle, horses, pigs and chickens in Japan. Parasitology International 63:638-639. doi:10.1016/j.parint.2014.04.003

Harada H, Takano Y, Shigeta Y. (2014) Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins. Journal of Chemical Physics 140:125103. doi: 10.1063/1.4869594

Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Shen JR, Nakajima T, Yamaguchi K. (2014) Large Scale QM/MM calculations of hydrogen bonding networks for proton transfer and water inlet channels for water
oxidation. – Functional Theoretical modelings of the oxygen evolving complex of photosystem II. Advances in Quantum Chemistry 7:325-413.

Shoji M, Hanaoka K, Ujiie Y, Tanaka W, Kondo D, Umeda H, Kamoshida Y, Kayanuma M, Kamiya K, Shiraishi K, Machida Y, Murakawa T, Hayashi H. (2014) A QM/MM Study of the l-Threonine Formation Reaction of Threonine Synthase:
Implications into the Mechanism of the Reaction Specificity. Journal of the American Chemical Society 136(12):4525-4533. doi:11.1021/ja408780c.