Recent publications written in English (since 2005)

2017

• Space as a Tool for Astrobiology: Review and recommendations for experimentations in Earth orbit and beyond
• Cottin H, Kotler JM, Billi D, Cockell C, Demets R, Ehrenfreund P, Elsaesser A, d'Hendecourt L, van Loon J, Martins Z, Onofri S, Quinn R, Rabbow E, Rettberg P, Ricco AJ, Slenzka K, de la Torre R, de Vera J-P, Westall F, Carrasco N, Fresneau A, Kawaguchi Y, Kebukawa Y, Nguyen D, Poch O, Saiagh K, Stalport F, Yamagishi A, Yano H, Klamm BA.
  Astrobiolgy in press (2017)
• Reconstructed ancestral enzymes suggest long-term cooling of Earth’s photic zone since the Archean.
• Garcia AK, Schopf JW, Yokobori S, Akanuma S, Yamagishi A.
  Proc. Natl. Acad. Sci. USA 114(18): 4619-4624 (2017) PubMed
• Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan
• Tokishita S, Shibuya H, Kobayashi T, Sakamoto M, Ha J-Y, Yokobori S, Yamagata H, Hanazato T.
  gene 611, 38-46 (2017) PubMed
• Updated mitochondrial phylogenomics of Pteriomorphia and Heterodonta in Bivalvia, including deep-sea chemosymbiotic Bathymodiolus mussels, vesicomyid clams, and the thyasirid clam Conchocele cf. bisecta.
• Ozawa M, Shimamura S, Takagi Y, Yokobori S, Maeda T, Maruyama T, Yoshida T.
  Marine Genomics 31, 43-52 (2017) PubMed
• Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific.
• Nitahara S, Kato S, Usui A, Urabe T, Suzuki K, Yamagishi A.
  PLOS ONE 12(2), e0173071, 10.1371/journal.pone.0173071(2017) PLOS ONE

2016

• Quest for ancestors of eukaryal cells based on phylogenetic analyses of aminoacyl tRNA synthetases
• Furukawa R, Nakagawa M, Kuroyanagi T, Yokobori S, Yamagishi A.
  J. Mol. Evol. 84(1): 51-66. (2016) PubMed
• Birth of Archaeal Cells—Molecular phylogenetic analyses of G1P dehydrogenase, G3P dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having G1P-polar lipids
• Yokobori S, Nakajima Y, Akanuma S, Yamagishi A.
  Archaea Article ID 1802675 (2016) Hindawi
• Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein
• Hashimoto T, Horikawa DD, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, Minakuchi Y, Ohishi K, Motoyama A, Aizu T, Abe K, Horiuchi T, Enomoto A, Kondo K, Tanaka S, Hara Y, Koshikawa S, Sagara H, Miura T, Yokobori S, Miyagawa K, Sugano S, Suzuki Y, Kubo T, Oyama M, Kohara Y, Fujiyama A, Arakawa K, Katayama T, Toyoda A, Kunieda T.
  Nature Comm. 7, 12808 (DOI: 10.1038/ncomms12808) (2016) Nature
• De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues
• Yagi S, Akanuma S, Yamagishi M, Uchida T, Yamagishi A.
  BBA-Proteins and Proteomics 1864(5): 479-487. (2016) PubMed Elsevier
• A novel large filamentous deltaproteobacterium on hydrothermally inactive sulfide chimneys of the Southern Mariana Trough
• Kato S, Yamagishi A.
  Deep-Sea Research Part I 110: 99-105 (2016) Elsevier
• Investigation of the interplanetary transfer of microbes in the Tanpopo mission at the Exposed Facility of the International Space Station
• Kawaguchi Y, Yokobori S, Hashimoto H, Yano H, Tabata M, Kawai H, Yamagishi A.
  Astrobiolgy 16(5):363-76 (2016) PubMed
• Chapter 20 “A Strategy for Designing Thermostable Enzymes by Reconstructing Ancestral Sequences Possessed by Ancient Life”
• Akanuma S. and Yamagishi A.
  Grand Challenges in Biology and Biotechnology “Biotechnology of Extremophiles: Advances and Challenges” ed. Pabulo H. Rampelotto, Springer p. 581-596 (2016)
• Chapter 20 "Ancestral Reconstruction of Enzymes"
• Akanuma S. and Yamagishi A.
  "Understanding enzymes; Function, Design, Engineering and Analysis" ed. Allan Svendsen, Pan Stanford Publishing (2016)

2015

• Evolution of eukaryotic DNA polymerases via interaction between cells and large DNA viruses
• Takemura M, Yokobori S, Ogata H.
  J. Mol. Evol. 81(1-2): 24-33 (2015) Springer PubMed
• Ultralow-density double-layer silica aerogel fabrication for the intact capture of cosmic dust in low-Earth orbits
• Tabata M, Kawai H, Yano H, Imai E, Hashimoto H, Yokobori S, Yamagishi A.
  J. Sol-Gel Sci. Tech. 77(2): 325-334 (2015) Springer
• Silica aerogel for capturing intact interplanetary dust particles for the Tanpopo experiment
• Tabata M, Yano H, Kawai H, Imai E, Kawaguchi Y, Hashimoto H, Yamagishi A.
  Orig. Life Evol. Biosph. 45, 225-229 (2015) PubMed Springer
• Ancestral amino acids substitution improves the thermal stability of recombinant lignin-peroxidase from white-rot fungi, Phanerochaete chrysosporium strain UAMH 3641
• Semba Y, Ishida M, Yokobori S, Yamagishi A.
  Protein Engineer. Des. Select. 28(7): 221-230. (2015) PubMed
• Impact frequency estimate of micron-sized meteoroids and debris on Tanpopo Capture Panels on the ISS
• Kurihara M, Higashide M, Takayanagi Y, Arai K, Yano H, Tabata M, Hasegawa S, Yamagishi A.
  Procedia Engineering 103, 334-340. (2015) Elsevier
• Potential for biogeochemical cycling of sulfur, iron and carbon within massive sulfide deposits below the seafloor
• Kato S, Ikehata K, Shibuya T, Urabe T, Ohkuma M, Yamagishi A.
  Environ. Microbiol. 17, 1817-1835 (2015) PubMed Wiley
• Epistasis effects of multiple ancestral-consensus amino acid substitutions on the thermal stability of glycerol kinase from Cellulomonas sp. NT3060
• Fukuda, Y, Abe A, Tamura T, Kishimoto T, Sogabe A, Akanuma S, Yokobori S, Yamagishi A, Imada K, Inagaki K.
  J. Biosci. Bioeng. (in press) PubMed Elsevier
• Robustness of predictions of extremely thermally stable proteins in ancient organisms
• Akanuma S, Yokobori S, Nakajima Y, Bessho M, Yamagishi A,
  Evol.69(11): 2954-2962(2015) PubMed Wiley
• Development of hydrothermal and frictional experimental systems to simulate sub-seafloor water-rock-microbe interactions. In Subseafloor biosphere linked to global hydrothermal systems: TAIGA concept
• Suzuki K, Kato S, Shibuya T, Hirose T, Fuchida S, Rejish Kumar VJ, Yoshizaki M, Masaki Y, Nakamura K, Kobayashi K, Masuda, H, Yamagishi A, Urabe T.
  In "Subseafloor biosphere linked to global hydrothermal systems: TAIGA concept" (Eds Ishibashi J, Okino K, Sunamura M). Tokyo: Springer Japan. pp 71-85. (2015) Springer
• Intra-field variation of prokaryotic communities on and below the seafloor in the back-arc hydrothermal system of the Southern Mariana Trough
• Kato S, Ohkuma M, Yamagishi A.
  In "Subseafloor biosphere linked to global hydrothermal systems: TAIGA concept" (Eds Ishibashi J, Okino K, Sunamura M), Tokyo: Springer Japan. pp 301-311. (2015) Springer
• Experimental assessment of microbial effects on chemical interactions between seafloor massive sulfides and seawater at 4°C.
• Kato S, Suzuki K, Shibuya T, Ishibashi J, Ohkuma M, Yamagishi A.
  In 2Subseafloor biosphere linked to global hydrothermal systems: TAIGA concept" (Eds Ishibashi J, Okino K, Sunamura M), Tokyo: Springer Japan. pp 95-103. (2015)

2014

• Computer Simulation Analysis of the Protein Binding Interfaces that Form a 4-Helix Bundle Motif
• Fukuda M, Yamada H, Morikawa R, Miyakawa T, Takasu M, Akanuma S, Yamagishi A.
  JPS Conf. Proc. 1, 016020 (2014) doi:10.1016/j.jbiosc.2014.03.002
• Coarse-Grained Molecular Dynamics Simulation of IPMDH
• Hirata Y, Komatsu Y, Fukuda M, Yamada H, Miyakawa T, Morikawa, R, Akanuma S, Yamagishi A, Takasu M.
  JPS Conf. Proc. 1, 016010 (2014) doi:10.1016/j.jbiosc.2014.03.002
• Chapter 3. Prokaryotes in metal deposits on the deep seafloor
• Kato S, Yamagishi A.
  In "Deep Sea, Edition 1" (Eds. Nigel T. Wilson), Nova Science Publishers Inc, pp. 103-134 (2014) href="http://www.ncbi.nlm.nih.gov/pubmed/25330135" target="_blank">PubMed Wiley
• Potential for biogeochemical cycling of sulfur, iron and carbon within massive sulfide deposits below the seafloor
• Kato S, Ikehata K, Shibuya T, Urabe T, Ohkuma M, Yamagishi A.
  Environ. Microbiol. (2014) doi:10.1111/1462-2920.12648 PubMed Wiley
• *Fluorescence imaging of microbe-containing particles shot from a two-stage Light-gas gun into an aerogel
• Kawaguchi Y, Sugino T, Tabata M, Okudaira K, Imai E, Yano H, Hasegawa S, Hashimoto H, Yabuta H, Kobayashi K, Kawai H, Mita H, Yokobori S, Yamagishi A.
  Orig. Life Evol. Biosph. (2014) doi:10.1007/s11084-014-9361-x Springer
• *Characterization of the low-temperature activity of Sulfolobus tokodaii glucose-1-dehydrogenase mutants
• Sugii T, Akanuma S, Yagi S, Yagyu K, Shimoda Y, Yamagishi A.
  J. Biosci. Bioeng. 118(4), 367-371 (2014) PubMed Elsevier
• *Addition of negatively charged residues can reverse the decrease in the solubility of an acidic protein caused by an artificially introduced non-polar surface patch
• Yagi S, Akanuma S, Yamagishi A.
  BBA Proteins and Proteomics 1844(3), 553-560 (2014) PubMed Elsevier
• Cloning and characterization of laccase DNA from the Royal Sun Medicinal Mushroom, Agaricus brasiliensis (Higher Basidiomycetes)
• Matsumoto-Akanuma A, Akanuma S, Motoi M, Yamagishi A, Ohno N.
  Int. J. Med. Mush. 16(4), 375-393 (2014)
• N-terminal hydrophobic amino acids of ATF5 confer IL-1β-induced stabilization
• Abe T, Kojima M, Akanuma S, Iwashita H, Yamazaki T, Okuyama R, Ichikawa K, Umemura M, Nakano H, Takahashi S, Takahashi Y.
  J. Biol. Chem. 289(7), 3888-3900 (2014)
• Preparation of Phi29 DNA polymerase free of amplifiable DNA using ethidium monoazide, an ultraviolet-free light-emitting diode lamp and trehalose
• Takahashi H, Yamazaki H, Akanuma S, Kanahara H, Saito T, Chimuro Kobayashi T, Ohtani T, Yamamoto K, Sugiyama S, Kobori T.
  PLoS ONE 9(2), e82624 (2014) PLos ONE 農研機構 時事通信
• Imaging live cell in micro-liquid enclosure by X-ray laser diffraction
• Kimura T, Joti Y, Shibuya A, Song C, Kim S, Tono K, Yabashi M, Tamakoshi M, Moriya T, Oshima T, Ishikawa T, Bessho Y, Nishino Y.
  Nat. Commun. 5, 3052 (2014) PubMed Nature.com 北大
• Arabidopsis thaliana mitochondrial EF-G1 functions in two different translational steps
• Suematsu T, Watanabe O, Kita K, Yokobori S, Watanabe Y.
  J. Biochem. 155(2), 107-114 (2014) PubMed
• Molecular Basis of ADP Inhibition of Vacuolar (V)-type ATPase/Synthase
• Kishikawa J, Nakanishi A, Furuike S, Tamakoshi M, Yokoyama K.
  J. Biol. Chem. 289(1), 403-412 (2014) PubMed
• Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation
• Fukuda M, Komatsu Y, Yamada H, Morikawa R, Miyakawa T, Takasu M, Akanuma S, Yamagishi A.
  Molecular Simulation 40(6), 498-503 (2014) T＆Fonline
• Coarse-Grained Molecular Dynamics Simulation of IPMDH
• Hirata Y, Komatsu Y, Fukuda M, Yamada H, Miyakawa T, Morikawa R, Akanuma S, Yamagishi A, Takasu M.
  JPS Conf. Proc. 1, 016010 (2014) doi:10.1016/j.jbiosc.2014.03.002 JPS
• Computer Simulation Analysis of the Protein Binding Interfaces that Form a 4-Helix Bundle Motif
• Fukuda M, Yamada H, Morikawa R, Miyakawa T, Takasu M, Akanuma S, Yamagishi A.
  JPS Conf. Proc. 1, 016020 (2014) doi:10.1016/j.jbiosc.2014.03.002 JPS
• Chapter 3. Prokaryotes in metal deposits on the deep seafloor
• Kato S, Yamagishi A.
  In "Deep Sea, Edition 1" (Eds. Nigel T. Wilson). Nova Science Publishers Inc, pp. 103-134 (2014)
• Chapter 2. How the early genetic code was established? -Inference from the analysis of extant animal mitochondrial decoding systems-
• Watanabe K, Yokobori S.
  In Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications (Eds. Erdmann VA, Markiewicz WT, Barciszewski J.) Springer-Verlag Berlin Heidelberg, pp. 25-40 (2014)

2013

• Distinct tRNA modifications in the thermo-acidophilic archaeon, Thermoplasma acidophilum
• Tomikawa C, Ohira T, Inoue Y, Kawamura T, Yamagishi A, Suzuki T, Hori H.
  FEBS Lett 587(21), 3575-3580 (2013)
• *The possible interplanetary transfer of microbes: Assessing the viability of Deinococcus spp. under the ISS environmental conditions for performing exposure experiments of microbes in Tanpopo mission
• Kawaguchi Y, Yang Y, Kawashiri N, Shiraishi K, Takasu M, Narumi I, Satoh K, Hashimoto H, Nakagawa K, Tanigawa Y, Momoki Y, Tanabe M, Sugino T, Takahashi Y, Shimizu Y, Yoshida S, Kobayashi K, Yokobori S, Yamagishi A.
  Origins of Life and Evolution of Biospheres 43(4-5), 411-428 (2013) PubMed Springer
• *Life without tRNA^Arg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
• Yokobori S, Kitamura A, Grosjean H, Bessho Y.
  Nucleic Acids Res 41: 6531-6543 (2013) PubMed
• Selection of lichens resistant to the cosmic environment - thermal cycle treatment, UV irradiation and heavy particle beam -
• Takahashi Y, Shibata S, Yokoyama J, Hashimoto H, Yokobori S, Yamagishi A.
  Biol. Sci. Space 27, 9-18 (2013)
• Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus thermophilus.
• Tani K, Arthur CP, Tamakoshi M, Yokoyama K, Mitsuoka K, Fujiyoshi Y, Gerle C.
  Microscopy (Oxf) 62(4), 467-474 (2013)
• Characteristics of microbial communities in crustal fluids in a deep-sea hydrothermal field of the suiyo seamount
• Kato S, Nakawake M, Kita J, Yamanaka T, Utsumi M, Okamura K, Ishibashi J, Ohkuma M, Yamagishi A.
  Front Microbiol 4, 85 (2013)
• *Experimental evidence for the thermophilicity of ancestral life
• Akanuma S, Nakajima Y, Yokobori S, Kimura M, Nemoto N, Mase T, Miyazono K, Tanokura M, Yamagishi A.
  Proc. Natl. Acad. Sci. USA 110 (27), 11067-11072 (2013) PubMed PNAS This Week in PNAS
• *Elemental dissolution experiments of basaltic rocks with ultra-pure water at 340C and 40MPa in a newly developed flow-type hydrothermal apparatus
• Kato S, Shibuya T, Nakamura K, Suzuki K, Rejish Kumar VJ, Yamagishi A.
  Geochemical Journal 47, 89-92 (2013)
• Decoding mechanism of non-universal genetic codes in Loligo bleekeri mitochondria
• Ohira T, Suzuki T, Miyauchi K, Suzuki T, Yokobori S, Yamagishi A, Watanabe K.
  J. Bio. Chem. 288, 7645-7652 (2013) PubMed
• Simulation study of protein-protein interfaces based on the 4-helix bundle structure
• Fukuda M, Komatsu Y, Morikawa R, Miyakawa T, Takasu M, Akanuma S, Yamagishi A.
  AIP Conf. Proc. 1518, 606-609 (2013)
• Simulation study of bacterial colonies formed by the twitching motility: the effect of slingshot-like motions of bacteria on the colony edge
• Morikawa R, Miyakawa T, Tamakoshi M, Takasu M
  AIP Conf. Proc. 1518, 590-593 (2013)
• Chapter 12.　Comparative Genomics of Thermophilic Bacteria and Archaea
• Akanuma S, Yokobori S, Yamagishi A.
  In "Thermophilic Microbes in Environmental and Industrial Biotechnology" (Eds. Satyanarayana, T., Litterchild J., Kawarabayasi, Y). Springer Science, pp. 331-349 (2013) Springer

2012

• Constructing protein nano-fiber and estimation of the electronic state around metal ions
• Komatsu Y, Fukuda M, Yamada H, Kawamoto S, Miyakawa T, Morikawa R, Takasu M, Yokojima S, Akanuma S, Yamagishi A.
  Int. J. Quant. Chem. 112, 3750-3755 (2012) Wiley
• Designing the binding surface of proteins to construct nano-fibers
• Komatsu Y, Yamada H, Kawamoto S, Fukuda M, Miyakawa T, Morikawa R, Takasu M, Akanuma S, Yamagishi A.
  Prog. Theor. Chem. Phys. 26, 555-567 (2012)
• Tolerance of eggs in the Tardigrade Ramazzottius varieornatus to extreme environments
• Horikawa, DD, Yamaguchi A, Sakashita T, Tanaka D, Hamada N, Yukuhiro F, Kuwahara H, Kunieda T, Watanabe M, Nakahara Y, Wada S, Funayama T, Katagiri C, Higashi S, Yokobori S, Kuwabara M, Rothschild LJ, Okuda T, Hashimoto H, Kobayashi Y.
  Astrobiol. 12, 283-289 (2012) PubMed
• *Prokaryotic abundance and community composition in a freshwater iron-rich microbial mat at circumneutral pH
• Kato S, Kikuchi S, Kashiwabara T, Takahashi Y, Suzuki K, Itoh T, Ohkuma M, Yamagishi A.
  Giomicrobiology Journal 29, 896-905 (2012) Taylor and Francis Online
• *Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers
• Kato S, Nakawake M, Ohkuma M, Yamagishi A.
  Extremophiles 16, 277-283 (2012) PubMed
• *Iron-based microbial ecosystem on and below the seafloor: a case study of hydrothermal fields of the Southern Mariana Trough
• Kato S, Nakamura K, Toki T, Ishibashi J, Tsunogai U, Hirota A, Ohkuma M, Yamagishi A.
  Front. Microbio. 3, 89 (2012) PubMed
• Formation, alteration and delivery of exogenous high molecular weight organic compounds: Objectives of the Tanpopo Mission from the point of view of chemical evolution
• Kobayashi K, Sarker PK, Ono K, Kawamoto Y, Obayashi Y, Kaneko T, Yoshida S, Mita H, Yabuta H, Yamagishi A.
  Trans. JSASS Aerospace Tech. Japan 10, Tp7-Tp11 (2012)

2011

• *Substitutions of coenzyme-binding, non-polar residues improve the low-temperature activity of thermophilic dehydrogenases
• Hayashi S, Akanuma S, Onuki W, Tokunaga C, Yamagishi A.
  Biochemistry 50, 8583-8593 (2011) PubMed ACS
• *Genomic and proteomic characterization of the large Myoviridae bacteriophage TMA of the extreme thermophile Thermus thermophilus
• Tamakoshi M, Murakami A, Sugisawa M, Tsuneizumi K, Takeda S, Saheki T, Izumi T, Akiba T, Mitsuoka K, Toh H, Yamashita A, Arisaka F, Hattori M, Oshima T, Yamagishi A.
  Bacteriophage 1, 152-164 (2011) PubMed Landes
• *Phylogeny-based design of a B-subunit of DNA gyrase and its ATPase domain using a small set of homologous amino acid sequences
• Akanuma S, Iwami S, Yokoi T, Nakamura N, Watanabe H, Yokobori S, Yamagishi A.
  J. Mol. Biol. 412, 212-225 (2011) PubMed ScienceDirect
• *Archaeal diversity in a terrestrial acidic spring field revealed by a novel PCR primer targeting archaeal 16S rRNA genes
• Kato, S., Itoh, T., Yamagishi, A.
  FEMS Microbiol. Lett. 319, 34-43 (2011) PubMed Wiley
• *Molecular characterization of the microbial community in hydrogenetic ferromanganese crusts of the Takuyo-Daigo Seamount, northwest Pacific
• Nitahara, S., Kato, S., Urabe, T., Usui, A., Yamagishi, A.
  FEMS Microbiol. Lett. 321, 121-129 (2011) PubMed Wiley
• *Stability of heterochiral hybrid membrane made of bacterial sn-G3P 2 lipids and archaeal sn-G1P Lipids
• Shimada, H., Yamagishi. A.
  Biochemistry 50, 4114-4120 (2011) PubMed ACS
• *Roles for the two N-terminal (beta/alpha) modules in the folding of a (beta/alpha)₈-barrel protein as studied by fragmentation analysis
• Akanuma S, Yamagishi A.
  Proteins 79, 221-231 (2011) PubMed Wiley
• The GINS complex from the thermophilic archaeon, Thermoplasma acidophilum may function as a homotetramer in DNA replication
• Ogino H, Ishino S, Mayanagi K, Haugland GT, Birkeland NK, Yamagishi A, Ishino Y.
  Extremophiles 15, 529-539 (2011) PubMed
• Male death resulting from hybridisation between subspecies of the gypsy moth, Lymantria dispar
• Higashiura, Y., H. Yamaguchi, M. Ishihara, N. Ono, H. Tsukagoshi, S. Yokobori, S. Tokishita, H. Yamagata, T. Fukatsu
  Heredity 106:603-613 (2011)
• Tanpopo cosmic dust collector: silica aerogel production and bacterial DNA contamination analysis
• Tabata. M., Y. Kawaguchi, S. Yokobori, H. Kawai, J. Takahashi, H. Yano, A. Yamagishi
  Biol .Sci. Space 25: 7-12. (2011)
• tRNA modification and genetic code variations in animal mitochondria
• Watanabe, K. S. Yokobori
  J. Nucleic Acids, doi:10.4061/2011/623095 (2011) PubMed
• Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria
• Suzuki T, Miyauchi K, Suzuki T, Yokobori SI, Shigi N, Kondow A, Takeuchi N, Yamagishi A, Watanabe K.
  J. Biol. Chem. 286, 35494-35498 (2011) PubMed
• Crystal Structures and Enzymatic Properties of a Triamine/Agmatine Aminopropyltransferase from Thermus thermophilus
• Ohnuma M, Ganbe T, Terui Y, Niitsu M, Sato T, Tanaka N, Tamakoshi M, Samejima K, Kumasaka T, Oshima T.
  J. Mol. Biol. 408, 971-86 (2011) PubMed ScienceDirect
• Calditerricola satsumensis gen. nov., sp. nov. and Calditerricola yamamurae sp. nov., extreme thermophiles isolated from a high-temperature compost
• Moriya, T., Hikota, T., Yumoto, I., Ito, T., Terui, Y., Yamagishi, A., Oshima, T.
  Int. J. System. Evol. Microbiol. 61, 631-636 (2011)
• Partial purification and characterization of polyphenoloxidase from Culinary-Medicinal Royal Sun Mushroom (the Himematsutake), Agaricus brasiliensis S. Wasser et al. (Agaricomycetideae)
• Matsumoto-Akanuma A, Akanuma S, Motoi M, Yamagishi A, Ohno N
  Int. J. Med. Mush. 13, 73-82 (2011) PubMed Begell house
• Chapter 16. Microbial biodiversity and biogeography on the deep seafloor.
• Kato S, Yamagishi A.
  In Changing Diversity in Changing Environment, (Grillo O, Venora G, eds.) Rijeka (2011) pp. 357-374. InTech
• Genetic code: Introduction (Version 2)
Watanabe, K. S. Yokobori
In: Encyclopedia of Life Science. DOI: 10.1002/9780470015902.a0000809 (2011)

2010

• *Microbial ecosystem in marine hydrothermal system in the early and present Earth
• Kato S, Yamagishi A.
  Viva Origino 38, 46-55 (2010) Viva Origino
• *Deinococcus aetherius sp. nov., isolated from the stratosphere.
• Yang, Y., T. Itoh, S. Yokobori, S. Itahashi, H. Shimada, K. Satoh, H. Ohba, I. Narumi, & A. Yamagishi.
  Internatl. J. Sys. Evol. Bacteriol. 60, 776-779 (2010) PubMed
• Search for microbes on the Mars surface with special interest in methane-oxidizing bacteria
• Yamagishi A., Yokobori, S., Yoshimura, Y., Yamashita, M., Hashimoto, H., Kubota, T., Yano, H., Haruyama, J., Tabata, M., Kobayashi, K., Honda, H., Utsumi, Y., Saiki, T., Itoh, T., Miyakawa, A., Hamase, K., Naganuma, T., Mita, H., Tonokura, K., Sasaki, S., and Miyamoto, H., Japan Astrobiology Mars Project (JAMP):
  Biological Sciences in Space 24, 67-82 (2010)
• Improvement of Bacillus circulans {beta}-amylase activity attained using the ancestral mutation method
• Yamashiro K, Yokobori SI, Koikeda S, Yamagishi A
  Protein Eng. Des. Sel. 23, 519-528 (2010) PubMed
• *Mimicking the evolution of a thermally stable monomeric four-helix bundle by fusion of four identical single-helix peptides
• Akanuma S, Matsuba T, Ueno E, Umeda N, Yamagishi A
  J. Biochem. 147, 371-379 (2010) PubMed Oxford Journals COVER
• *Biogeography and biodiversity in sulfide structures of active and inactive vents at deep-sea hydrothermal fields of the Southern Mariana Trough
• Kato S, Takano Y, Kakegawa T, Oba H, Inoue K, Kobayashi C, Utsumi M, Marumo K, Kobayashi K, Ito Y, Ishibashi J, Yamagishi A
  Applied and Environmental Microbiology 76, 2968-2979 (2010). PubMed Journals.ASM.org
• A bacterial elongation factor G homolog exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi
• Suematsu T, S Yokobori, H Morita, S Yoshinari, T Ueda, K Kita, N Takeuchi, Y. Watanabe
  Mol. Microbiol. 75: 1445-1454 (2010) PubMed
• Transcription profile of Thermus thermophilus CRISPR systems after phage infection.
• Agari Y, Sakamoto K, Tamakoshi M, Oshima T, Kuramitsu S, Shinkai A.
  J. Mol. Biol. 395: 270-281. (2010) pubmed

2009

• *Abundance of Zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough
• Kato S, Yanagawa K, Sunamura M, Takano Y, Ishibashi J-i, Kakegawa T, Utsumi M, Yamanaka T, Toki T, Noguchi T, Kobayashi K, Moroi A, Kimura H, Kawarabayasi Y, Marumo K, Urabe T, Yamagishi A
  Environmental Microbiology 11, 3210-3222 (2009) PubMed Wiley-Blackwell
• *Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the southern Mariana Trough
• Kato S, Kobayashi C, Kakegawa T, Yamagishi A
  Environmental Microbiology 11, 2094-2111 (2009) PubMed Wiley-Blackwell
• *Spatial distribution, diversity and composition of bacterial communities in sub-seafloor fluids at a deep-sea hydrothermal field of the Suiyo Seamount
• Kato S, Hara K, Kasai H, Teramura T, Sunamura M, Ishibashi J-i, Kakegawa T, Yamanaka T, Kimura H, Marumo K, Urabe T, Yamagishia A.
  Deep Sea Research Part I: Oceanographic Research Papers 56, 1844-1855 (2009) ScienceDirect
• Significance of Organic Compounds in Interplanetary Dust Particles: Scientific Objectives of Tanpopo Mission
• Kobayashi K, Hashimoto H, Kaneko T, Mita H, Nakashima S, Naraoka H, Okudaira K, Takahashi J, Takano Y, Yamagishi A, Yamashita M, Yano H, Yokobori S, Tanpopo WG.
  Orig. Life Evol. Biosph. 39, 4 (2009)
• *Bacterial survival in responses to desiccation and high huminity at above zero and subzero temperatures.
• Yang Y, Yokobori S, Yamagishi A.
  Adv. Space Res. 43,1285-1290(2009)
• *Assessing Panspermia hypothesis by microorganisms collected from the high altitude atmosphere.
• Yang Y, Yokobori S. Yamagishi A.
  Biol. Sci. Space. 23, 151-163 (2009) Full Text
• *Deinococcus aerius sp. nov., isolated from the high atmosphere.
• Yang Y, Itoh T, Yokobori S, Itahashi S, Shimada H, Satoh K, Ohba H, Narumi I, Yamagishi A
  Internatl. J. Sys. Evol. Bacteriol. 59, 1862-1866 (2009)
• TANPOPO: Astrobiology Exposure and Micromeeoroid Capture Experiments For Understanding Survival Possibility of Trans-Space Migration of Microorganisms.
• Yokobori S, Yamagishi A, Yang Y, Fujisaki K, Hashimoto H, Kawai H, Kobayashi K, Mita H, Okudaira K, Tabata M, Yano H, Yamashita M, Yoshimura Y, Tanpopo WG.
  Orig. Life Evol. Biosph.39,64-65 (2009)
• *Gain and loss of an intron in the protein-coding gene in Archaea
• Yokobori S, Itoh T, Yoshinari S, Nomura N, Sako Y, Yamagishi A, Oshima T, Kita K, Watanabe Y.
  BMC Evol. Biol.. 9, 198 (2009) PubMed
• Potential speciation of morphotypes in the photosymbiotic ascidian Didemnum molle in the Ryukyu Archipelago, Japan
• Hirose, M., S. Yokobori, E. Hirose
  Coral Reefs 28: 119-126 (2009) PubMed
• Induction profile of HSP70-cognate genes by environmental pollutants in Chironomidae.
• Yoshimi T, K Odagiri, S Yokobori, Y Takahashi, Y Sugaya, T Miura
  Environ. Toxic. Pharmacol. 28: 294-301 (2009) PubMed

2008

• *Experimental evidence for the existence of a stable half-barrel subdomain in the (beta/alpha)₈-barrel fold.
• Akanuma S, Yamagishi A.
  J. Mol. Biol. 382(2):458-466 (2008) PubMed ScienceDirect
• *Random mutagenesis improves the low-temperature activity of the tetrameric 3-isopropylmalate dehydrogenase from the hyperthermophile Sulfolobus tokodaii.
• Sasaki M, Uno M, Akanuma S, Yamagishi A.
  Protein Eng.Des.Sel. 21,(12):721-727(2008) PubMed Oxford Journals COVER
• *Effects of pH and temperature on composition of polar lipids in Thermoplasma acidophilum HO-62.
• Shimada H, Nemoto N, Shida Y, Oshima T, Yamagishi A
  J. Bacteriol. 190: 5405-5411(2008) PubMed
• Prebiotic origin of glycolytic metabolism: histidine and cysteine can produce acetyl CoA from glucose via reactions homologous to non-phosphorylated Entner-Doudoroff pathway.
• Shimizu M, Yamagishi A, Kinoshita K, Shida Y, Oshima T.
  J. Biochem. 144, 383-388 (2008) PubMed
• Solvent site-dipole field accompanying protein-ligand approach process.
• Takano N, Umezawa J, Ikebe K, Sonobe Y, Yagisawa R, Ito J, Hamasaki N, Mitomo D, Miyagawa H, Yamagishi A, Higo J
  Chem-Bio. Informatics J. 8�F14-24(2008) PubMed
• TANPOPO: astrobiology exposure and micrometeoroid capture experiments.
• Yamagishi A., Yano H., Kobayashi K., Yokobori S., Tabata M., Kawai H., Yamashita M., Hashimoto H., Naraoka H. and Mita H.
  International Symposium on Space Technology and Science (ISTS) Web Paper Archives. 2008-k-05 (2008)
• *UV-resistant Bacteria isolated from upper troposphere and lower stratosphere.
• Yang Y. Itahashi S., Yokobori S. and Yamagishi A.
  Biol.Sci.Space 22:18-25 (2008)
• *Investigation of cultivable microorganisms in the stratosphere collected by using a balloon in 2005.
• Yang Y, Yokobori S, Kawaguchi J, Yamagami T, Iijima N, Izutsu H, Fuke Y, Saitoh S, Matsuzaka M, Namiki S, Ohta M, Toriumi K, Yamada I, Seo M, Yamagishi A
  JAXA-RR-08-001,35-42 (2008)
• *Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: Implications for lophotrochozoan phylogeny.
• Yokobori S, Iseto T, Asakawa S, Sasaki T, Shimizu N, Yamagishi A, Oshima T, Hirose E
  Molecular Phylogenetics and Evolution 47:612-628 (2008) PubMed
• Methods for reducing nonspecific interaction in antibody-antigen assay via atomic force microscopy.
• Wakayama J, Sekiguchi H, Akanuma S, Ohtani T, Sugiyama S
  Anal Biochem. 380:51-58 (2008) PubMed
• ATP Hydrolysis and Synthesis of a Rotary Motor V-ATPase from Thermus thermophilus.
• Nakano M, Imamura H, Toei M, Tamakoshi M, Yoshida M, Yokoyama K.
  J Biol Chem. 25;283(30):20789-20796 (2008) pubmed
• Molecular mechanism of energy conservation in polysulfide respiration.
• Jormakka M, Yokoyama K, Yano T, Tamakoshi M, Akimoto S, Shimamura T, Curmi P, Iwata S.
  Nat. Struct. Mol. Biol. 15:730-737 (2008) pubmed

2007

• *Extremely Thermophilic Translation System in the Common Ancestor Commonote: Ancestral Mutants of Glycyl-tRNA Synthetase from the Extreme Thermophile Thermus thermophilus.
• Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A.
  J Mol Biol. (2007) 369(4):1060-9 PubMed
• *An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin.
• Hara F, Yamashiro K, Nemoto N, Ohta Y, Yokobori S, Yasunaga T, Hisanaga S, Yamagishi A.
  J Bacteriol. (2007) 189(5):2039-45 PubMed
• *The effects of mutations at position 253 on the thermostability of the Bacillus subtilis 3-isopropylmalate dehydrogenase subunit interface.
• Ohkuri T, Yamagishi A
  J.Biochem.141:791-797 (2007) PubMed
• "Purification and characterization of pepsinogens from the gastric mucosa of African coelacanth, Latimeria chalumnae, and properties of the major pepsins."
• Tanji, M., E. Yakabe, T. Kageyama, S. Yokobori, M. Ichinose, K. Miki, H. Ito, K. Takahashi
  Comparative Biochem. Physiol. 146(3):412-20. (2007) pubmed
• Dodecamer rotor ring defines H+/ATP ratio for ATP synthesis of prokaryotic V-ATPase from Thermus thermophilus.
• Toei M, Gerle C, Nakano M, Tani K, Gyobu N, Tamakoshi M, Sone N, Yoshida M, Fujiyoshi Y, Mitsuoka K, Yokoyama K.
  Proc. Natl. Acad. Sci. USA 104:20256-20261(2007) pubmed

2006

• DNA-protein binding mediated by solvent site-dipole field.
• Hamasaki, N., Miyagawa, H., Mitomo, D., Yamagishi, A. and Higo, J.
  Chemical physics Lett. (2006) 431: 160-163
• Cloning and Characterization of Polyphenoloxidase DNA from Agaricus brasiliensis S. Wasser et al. (Agaricomycetideae) .
• Matsumoto-Akanuma A, Yamagishi A, Motoi A, Ohno N.
  International Journal of Medicinal Mushrooms (2006), 8(1), 67-76.
• Thermostable proteins designed by using phylogenetic trees.
• Yamagishi A, Watanabe K, Shimizu H, Ohkuri T, Yokobori S
  In Proceedings of the International Symposium on Extremophiles and Their Applications 2005. (2006)
• Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease.
• Yoshinari S, Itoh T, Hallam SJ, DeLong EF, Yokobori S, Yamagishi A, Oshima T, Kita K, Watanabe Y.
  Biochem. Biophys. Res. Commun. 346, 1024-1032 (2006) PubMed
• *The effects of multiple ancestral residues on the Thermus thermophilus 3-isopropylmalate dehydrogenase.
• Watanabe K, Yamagishi A.
  FEBS Lett. 580: 3867-3871 (2006) PubMed
• Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model.
• Mitomo D, Nakamura H, Ikeda K, Yamagishi A, Higo J
  Proteins. 64(4):883-94. (2006) PubMed
• *Structural analysis of the plasmid pTA1 isolated from the thermoacidophilic archaeon Thermoplasma acidophilum.
• Yamashiro, K, Yokobori S, Oshima T, Yamagishi A
  Extremophiles 10: 327-335 (2006) PubMed
• *Designing thermostable proteins: Ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree.
• Watanabe K, Ohkuri T, Yokobori S, Yamagishi A
  J. Mol. Biol. 355, 664-674 (2006) PubMed
• Two-dimensional crystallization and analysis of projection images of intact�@Thermus thermophilus V-ATPase.
• Gerle C, Tani K, Yokoyama K, Tamakoshi M, Yoshida M, Fujiyoshi Y, Mitsuoka K
  J. Struct. Biol. 153:200-206 (2006) pubmed
• The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus: a purine36G37 sequence in tRNA is recognized by the enzyme
• Takeda, H., T. Yokooka, Y. Ikeuchi, S. Yokobori, K. Okadome, F. Takano, T. Oshima, T. Suzuki, Y. Endo, H. Hori
  Genes to Cells 11: 1353-1365 (2006) pubmed
• Multiple origins of the ascidian-Prochloron symbiosis: Molecular phylogeny of photosymbiotic and non-symbiotic colonial ascidians inferred from 18S rDNA sequences
• Yokobori S, A Kurabayashi, BA Neilan, T Maruyama, E Hirose
  Mol. Phylogen. Evol. 40: 8-19 (2006) pubmed

2005

• *Identification and characterization of key substructures involved in the early folding events of a (beta/alpha)8-barrel protein as studied by experimental and computational methods
• Akanuma S, Yamagishi A.
  J. Mol. Biol. 353, 1161-1170 (2005) PubMed
• *A detailed unfolding pathway of a (beta/alpha)8-barrel protein as studied by molecular dynamics simulations.
• Akanuma S, Miyagawa H, Kitamura K, Yamagishi A.
  Proteins. 2005 Feb 15;58(3):538-46. PubMed
• *Characterization of the DNA gyrase from the thermoacidophilic archaeon Thermoplasma acidophilum
• Yamashiro K, Yamagishi A
  J. Bacteriol. 187, 8531-8536 (2005) PubMed
• In situ Ore formation experiment: Amino acids and amino sugars trapped in artificial chimneys on deep-sea hydrothermal systems at Suiyo Seamount, Izu-Bonin Arc, Pacific Ocean.
• Takano Y, Marumo Y, Ebashi T, Gupta LP, Kawahata H, Kobayashi K, Yamagishi A, Kuwabara T
  Bull. Chem. Soc. Japan. 78: 638-651 (2005).
• *Analysis of the Archaeal Sub-Seafloor Community at Suiyo Seamount on the Izu-Bonin Arc
• Hara K, Kakegawa T, Yamashiro K, Maruyama A, Ishibashi J, Marumo K, Urabe T, Yamagishi A
  Advances in Space Research, 35(9), 1634-1642 (2005). PubMed
• Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria.
• Shirai T, Nakato A, Izutani N, Nagahisa K, Shioya S, Kimura E, Kawarabayasi Y, Yamagishi A, Gojobori T, and Shimizu H.
  Metab Eng. 2005 Mar;7(2):59-69. PubMed
• *Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase.
• Hisako Iwabata, Keiko Watanabe, Takatoshi Ohkuri, Shin-ichi Yokobori, and Akihiko Yamagishi.
  2005, FEMS Microbilo. Lett. 243:393-398 PubMed
• Structure of a central stalk subunit F of V-type ATPase/synthase from Thermus thermophilus.
• Makyio, H., Iino, R., Ikeda, C., Imamura, H., Tamakoshi, M., Iwata, M., Stock, D., Bernal, R. A., Yoshida, M., Yokoyama, K., and Iwata, S.
  EMBO J. 24:3974-3983 (2005)pubmed
• N1-aminopropylagmatine: A new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus.
• Ohnuma, M., Terui, Y., Tamakoshi, M., Mitome, H., Niitsu, M., Samejima, K., Kawashima, E., and Oshima, T.
  J. Biol. Chem. 280:30073-30082 (2005)pubmed
• Functional reconstitution of a crenarchaeal splicing endonuclease in vitro.
• Yoshinari, S., S. Fujita, R. Masui, S. Kuramitsu, S. Yokobori, K. Kita, Y. Watanabe
  Biochem. Biophys. Res. Com. 334: 1254-1259 (2005) pubmed
• The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.
• Matsubara, M., M. Komatsu, T. Araki, S. Asakawa, S. Yokobori, K. Watanabe, H. Wada
  Mol. Phylogenet. Evol. 36: 598-605 (2005) pubmed
• *Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates.
• Yokobori, S., T. Oshima, H. Wada
  Mol. Phylogenet. Evol. 34: 273-283 (2005) pubmed