Tokyo University of Agriculture and Technology Biomolecular Engineering & Marine Biotechnology Lab.

publicationsArticles

2025
  1. A. Hanada, T. Kasuga, M. Iwamoto, A. Mizusawa, S. Murata, T. Aketo, K. Hirata, K. Kataoka, A. Arakaki, N. Ohkama-Ohtsu, T. Tanaka “Combined use of phosphorus containing calcium silicate and phosphate-solubilizing bacterium as a solid biofertilizer for sustainable soybean cultivation."J. Biosci. Bioeng., (2025)
2024
  1. D. Montroni, E. Sarmiento, R. Zhao, P. S. Dasika, J. M. Connolly, R. Wuhrer, Y. Zhang, M. Zhernenkov, T. Wang, B. P. Ramirez‐Santana, L. Sheppard, O. H. Avila‐Poveda, A. Arakaki, M. Nemoto, P. Zavattieri, D. Kisailus “The Multiphasic Teeth of Chiton Articulatus, an Abrasion‐Resistant and Self‐Sharpening Tool for Hard Algae Collection."Adv. Funct. Mater., 34, 2401658 (2024)
2023
  1. J. Lee, J. Connolly, W. Yang, G. Freychet, T. Wang, S. A. Herrera, S. Murata, P. S. Dasika, D. Montroni, A. Pohl, C. Zhu, M. Zhernenkov, R. Wuhrer, L. Sheppard, M. Nemoto, A. Arakaki, P. Zavattieri, D. Kisailus “Fibrous anisotropy and mineral gradients within the radula stylus of chiton: Controlled stiffness and damage tolerance in a flexible biological composite."J. Compos. Mater., 57, 565-574 (2023)
  2. R. Tomoe, K. Fujimoto, T. Tanaka, A. Arakaki, D. Kisailus, T. Yoshino “Lipid membrane modulated control of magnetic nanoparticles within bacterial systems."J. Biosci. Bioeng., 136, 253-260 (2023)
2022
  1. W. Huang, D. Montroni, T. Wang, S. Murata, A. Arakaki, M. Nemoto, D. Kisailus “Nanoarchitected tough biological composites from assembled chitinous scaffolds."Acc Chem Res., 55, 1360-1371 (2022)
  2. T. Wang, W. Huang, C. H. Pham, S. Murata, S. Herrera, N. D. Kirchhofer, B. Arkook, D. Stekovic, M. E. Itkis, N. Goldman, L. Zepeda-Ruiz, G. Freychet, M. Zhernenkov, M. Nemoto, A. Arakaki, D. Kisailus “Mesocrystalline Ordering and Phase Transformation of Iron Oxide Biominerals in the Ultrahard Teeth of Cryptochiton stelleri."Small Struct., 3, 2100202 (2022)
  3. S. Murata, J. Rivera, M. Y. Noh, N. Hiyoshi, W. Yang, D. Y. Parkinson, H. S. Barnard, Y. Arakane, D. Kisailus, A. Arakaki “Unveiling characteristic proteins for the structural development of beetle elytra."Acta Biomater., 140, 467-480 (2022)
  4. K. Arai, S. Murata, T. Wang, W. Yoshimura, M. Oda-Tokuhisa, T. Matsunaga, D. Kisailus, A. Arakaki “Adsorption of Biomineralization Protein Mms6 on Magnetite (Fe3O4) Nanoparticles."Int. J. Mol. Sci., 23, 5554 (2022)
  5. T. Yoshino, Y. Mao, Y. Maeda, R. Negishi, S. Murata, S. Moriya, H. Shimada, A. Arakaki, K. Kobayashi, Y. Hagiwara, K. Okamoto, T. Tanaka “Single‐cell genotyping of phytoplankton from ocean water by gel‐based cell manipulation."Biotechnol. J., 17, 2100633 (2022)
2021
  1. J. Rivera, S. Murata, M. S. Hosseini, A. A. Trikanad, R. James, A. Pickle, N. Yaraghi, N. Matsumoto, W. Yang, D. Y. Parkinson, H. S. Barnard, P. Zavattieri, A. Arakaki, D. Kisailus “Structural design variations in beetle elytra."Adv. Funct. Mater., 31, 2106468 (2021)
2020
  1. J. Rivera, M.S. Hosseini, D. Restrepo, S. Murata, D.Y. Parkinson, H.S. Barnard, A. Arakaki, P. Zavattieri, D. Kisailus “Toughening mechanisms of the elytra of the diabolical ironclad beetle."Nature, 586, 543-548 (2020)
  2. A. Arakaki, M. Goto, M. Maruyama, T. Yoda, M. Tanaka, A. Yamagishi, Y. Yoshikuni, T. Matsunaga “Restoration and modification of magnetosome biosynthesis by internal gene acquisition in a magnetotactic bacterium."Biotechnol. J, 15, 2000278 (2020)
  3. G. Mirabello, A. Ianiro, P.H.H. Bomans, T. Yoda, A. Arakaki, H. Friendrich, G. de With, N.A.J.M. Sommerdijk “Crystallization by particle attachment is a colloidal assembly process."Nat. Mater., 19, 391-396 (2020)
  4. A. Pohl, S.A. Herrera, D. Restrepo, R. Negishi, J.-Y. Jung, C. Salinas, R. Wuhrer, T. Yoshino, J. McKittrick, A. Arakaki, M. Nemoto, P. Zavattieri, D. Kisailus “Radular stylus of Cryptochiton stelleri: a multifunctional lightweight and flexible fiber-reinforced composite."J. Mech. Behav. Biomed. Mater., 111, 103991 (2020)
  5. A. Arakaki, T. Matsumoto, N. Shimura, Y. Maeda, T. Yoshino, M. Matsumoto, D. Kisailus, T. Tanaka “Analysis of UV irradiation-induced cell settling of an oleaginous diatom, Fistulifera solaris, for efficient biomass recovery."Algal. Res, 47, 101834 (2020)
2019
  1. T. Wang, A. Arakaki, D. Kisailus “Template-free synthesis of Ta3N5 hollow nanospheres as a visible-light-driven photocatalyst."J. Phys. Commun., 3, 75010 (2019)
2018
  1. M. Tanaka, T. Suwatthanarak, A. Arakaki, B.R.G. Johnson, S.D. Evans, M. Okochi, S. Staniland, T. Matsunaga “Enhanced tubulation of liposome containing cardiolipin by MamY protein from magnetotactic bacteria."Biotechnol. J, 13, 1800087 (2018)
  2. T. Tanaka, O. Nogariya, N. Shionoiri, Y. Maeda, A. Arakaki “Integrated molecular analysis of the inactivation of a non-enveloped virus, feline calicivirus, by UV-C radiation."J. Biosci. Bioeng., 126, 63-68 (2018)
2017
  1. A. Arakaki, S. Nakata, T. Tokuhisa, Y. Ogawa, K. Sato, T. Sonoi, S.P. Donachie, T. Matsunaga “Quantitative and time-course analysis of 1H,1H,2H,2H,8H,8H-perfluorododecanol microbial degradation in activated sludge."Appl. Microbiol. Biotechnol., 101, 8259-8266 (2017)
  2. A. Arakaki, T. Matsumoto, T. Tateishi, M. Matsumoto, D. Nojima, Y. Tomoko, T. Tanaka “UV-C irradiation accelerates neutral lipid synthesis in the marine oleaginous diatom Fistulifera solaris."Biores. Technol., 245, 1520-1526 (2017)
2016
  1. A. Yamagishi, K. Narumiya, M. Tanaka, T. Matsunaga, A. Arakaki “Core amino acid residues in the morphology-regulating protein, Mms6, for intracellular magnetite biomineralization."Sci. Rep., 6, 35670 (2016)
  2. A. Arakaki, D. Kikuchi, M. Tanaka, A. Yamagishi, T. Yoda, T. Matsunaga “Comparative subcellular localization analysis of magnetosome proteins reveals a unique localization behavior of Mms6 protein onto magnetite crystals."J. Bacteriol., 198, 2794-2802 (2016)
  3. A. Yamagishi, M. Tanaka, J.M.M. Lenders, J. Thiesbrummel, N.A.J.M. Sommerdijk, T. Matsunaga, A. Arakaki “Control of magnetite nanocrystal morphology in magnetotactic bacteria by regulation of mms7 gene expression."Sci. Rep., 6, 29785 (2016)
  4. M. Tanaka, W. Knowles, R. Brown, N. Hondow, A. Arakaki, S. Baldwin, S. Staniland, T. Matsunaga “Biomagnetic recovery and bioaccumulation of selenium granules in magnetotactic bacteria."Appl. Environ. Microbiol., 82, 3886-3891 (2016)
  5. A. Arakaki, M. Takahashi, M. Hosokawa, T. Matsunaga, T. Tanaka “Bacterial inactivation by applying an alternating electromagnetic field using PAMAM dendron-modified magnetic nanoparticles."Electrochemistry, 84, 324-327 (2016)
2015
  1. T. Tokuhisa, M. Kawasaki, D. Kisailus, M. Yuda, T. Matsunaga, A. Arakaki “Crystal growth of aspirin using a temperature-controlled microfluidic device."Cryst. Growth Des., 15, 4549-4555 (2015)
  2. A. Kanazawa, K. Satoh, S. Kanaoka, M. Kakihana, M. Kobayashi, J. Sato, H. Imai, Y. Oaki, A. Arakaki, K. Katagiri, M. Kamigaito, S. Aoshima “Controlled radical polymerization of styrene with magnetic iron oxides prepared through hydrothermal, bioinspired, and bacterial processes."RSC Adv., 5, 51122-51129 (2015)
  3. J.J.M. Lenders, H.R. Zope, A. Yamagishi, P.H.H. Bomans, A. Arakaki, A. Kros, G. de With, N.A.J.M. Sommerdijk “Bioinspired magnetite crystallization directed by random copolypeptides."Adv. Funct. Mater., 25, 711-719 (2015)
2014
  1. J.J.M. Lenders, C.L. Altan, P.H.H. Bomans, A. Arakaki, S. Bucak, G. de With, N.A.J.M. Sommerdijk “Bio-inspired co-precipitation method for the controlled synthesis of magnetite nanoparticles."Cryst. Growth Des., 14, 5561-5568 (2014)
  2. A. Arakaki, A. Yamagishi, A. Fukuyo, M. Tanaka, T. Matsunaga “Co-ordinated functions of Mms proteins define the surface structure of cubo-octahedral magnetite crystals in magnetotactic bacteria."Mol. Microbiol., 93, 554-567 (2014)
  3. A. Arakaki, A. Yamagishi, T. Matsunaga “Protein-mediated morphological regulation of magnetite crystal in magnetotactic bacteria."J. Jpn. Soc. Powder Powder Metallurgy, 61, S99-S103 (2014)
  4. T. Takamura, T. Tashiro, A. Arakaki, A. Sandhu “Functionalization of magnetotactic bacteria for microrobotic applications."IEEE Tran. Magn., 50, 4700202 (2014)
2013
  1. A. Arakaki, D. Iwama, Y. Liang, N. Murakami, M. Ishikura, T. Tanaka, T. Matsunaga “Glycosylceramides from marine green microalga, Tetraselmis sp.."Phytochemistry, 85, 107-114 (2013)
2012
  1. A. Kanazawa, S. Kanaoka, N. Yagita, Y. Oaki, H. Imai, M. Oda, A. Arakaki, T. Matsunaga, S. Aoshima “Biologically synthesized or bioinspired process-derived iron oxides as catalysts for living cationic polymerization of a vinyl ether."Chem. Commun., 48, 10904-10906 (2012)
  2. D. Baba, Y. Seiko, T. Nakanishi, H. Zhang, A. Arakaki, T. Matsunaga, T. Osaka “Effect of magnetite nanoparticles on living rate of MCF-7 human breast cancer cells."Coll. Surf. B: Biointerfaces, 95, 254-257 (2012)
  3. T. Tanaka, K. Shibata, M. Hosokawa, K. Hatakeyama, H. Gomyo, A. Arakaki, T. Mogi, T. Taguchi, H. Wake, T. Tanaami, T. Matsunaga “Characterization of magnetic nanoparticles modified with thiol core, functionalized PAMAM dendron for DNA recovery."J. Colloid Interface Sci., 377, 469-475 (2012)
  4. A. Arakaki, K. Shibata, T. Mogi, M. Hosokawa, K. Hatakeyama, H. Gomyo, T. Taguchi, H. Wake, T. Tanaami, T. Matsunaga, T. Tanaka “Efficient DNA release from PAMAM dendrimer-modified superparamagnetic nanoparticles for DNA recovery."Polym. J., 44, 672-677 (2012)
  5. M. Tanaka, R. Brown, N. S. Hondow, A. Arakaki, T. Matsunaga, S. S. Staniland “Highest levels of Cu, Mn and Co doped into nanomagnetic magnetosomes through optimized biomineralisation."J. Mater. Chem., 22, 11919-11921 (2012)
2011
  1. M. Matsumoto, D. Iwama, A. Arakaki, A. Tanaka, T. Tanaka, H. Miyashita, T. Matsunaga “Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from marine sediments."Int. J. Syst. Evol. Microbiol., 61, 2956-2961 (2011)
  2. J. M. Galloway, A. Arakaki, F. Masuda, T. Tanaka, T. Matsunaga, S. S. Staniland “Magnetic bacterial protein Mms6 controls morphology, crystallinity and magnetism of cobalt-doped magnetite nanoparticles in vitro."J. Mater. Chem., 21, 15244-15254 (2011)
  3. M. Tanaka, E. Mazuyama, A. Arakaki, T. Matsunaga “MMS6 protein regulates crystal morphology during nano-sized magnetite biomineralization in vivo."J. Biol. Chem., 286, 6386-6392 (2011)
2010
  1. A. Arakaki, Y. Ishii, T. Tokuhisa, S. Murata, K. Sato, T. Sonoi, H. Tatsu, T. Matsunaga “Microbial biodegradation of a novel fluorotelomer alcohol, 1H,1H,2H,2H,8H,8H-perfluorododecanol, yields short fluorinated acids."Appl. Microbiol. Biotechnol., 88, 1193-1203 (2010)
  2. M. Hosokawa, T. Hayata, Y. Fukuda, A. Arakaki, T. Yoshino, T. Tanaka, T. Matsunaga “Size-selective microcavity array for rapid and efficient detection of circulating tumor cells."Anal. Chem., 82, 6629-6635 (2010)
  3. A. Arakaki, M. Shibusawa, M. Hosokawa, T. Matsunaga “Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple displacement amplification."Appl. Environ. Microbiol., 76, 1480-1485 (2010)
  4. M. Tanaka, A. Arakaki, S. S. Staniland, T. Matsunaga “Simultaneously discrete biomineralization of magnetite and tellurium nanocrystals in magnetotactic bacteria."Appl. Environ. Microbiol., 76, 5526-5532 (2010)
  5. M. Tanaka, A. Arakaki, T. Matsunaga “Identification and functional characterization of liposome tubulation protein from magnetotactic bacteria."Mol. Microbiol., 76, 480-488 (2010)
  6. A. Arakaki, K. Ooya, Y. Akiyama, M. Hosokawa, M. Komiyama, A. Iizuka, K. Yamaguchi, T. Matsunaga “TCR-β repertoire analysis of antigen-specific single T cells using a high-density microcavity array."Biotechnol. Bioeng., 106, 311-318 (2010)
  7. A. Arakaki, F. Masuda, Y. Amemiya, T. Tanaka, T. Matsunaga “Control of the morphology and size of magnetite particles with peptides mimicking the Mms6 protein from magnetotactic bacteria."J. Colloid Interface Sci., 343, 65-70 (2010)
  8. T. Abe, S. Ito, N. Nishi, Y. Tsukada, T. Yasunaga, A. Arakaki, T. Matsunaga, M. Yohda “Structure and function of small heat shock proteins from the magnetotactic bacterium Magnetospirillum magneticum AMB-1."Kobunshi Ronbunshu, 67, 698-704 (2010)
2009
  1. H. Nakazawa, A. Arakaki, S. Narita-Yamada, I. Yashiro, K. Jinno, N. Aoki, A. Tsuruyama, Y. Okamura, S. Tanikawa, N. Fujita, H. Takeyama, T. Matsunaga “Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria."Genome Res., 19, 1801-1808 (2009)
  2. M. Hosokawa, A. Arakaki, M. Takahashi, T. Mori, H. Takeyama, T. Matsunaga “High-density microcavity array for cell detection: single-cell analysis of hematopoietic stem cells in peripheral blood mononuclear cells."Anal. Chem., 81, 5308-5313 (2009)
  3. T. Matsunaga, M. Nemoto, A. Arakaki, M. Tanaka “Proteomic analysis of irregular bullet-shaped magnetosomes in the sulfate-reducing bacterium."Proteomics, 9, 3341-3352 (2009)
  4. A. Arakaki, F. Masuda, T. Matsunaga “Iron oxide crystal formation on a substrate modified with the Mms6 protein from magnetotactic bacteria."Mater. Res. Soc. Symp. Proc., 1187, KK03-08 (2009)
2008
  1. T. Matsunaga, M. Hosokawa, A. Arakaki, T. Taguchi, T. Mori, T. Tanaka, H. Takeyama “High-efficiency single-cell entrapment and fluorescence in situ hybridization analysis using a poly(dimethylsiloxane) microfluidic device integrated with a black poly(ethylene terephthalate) micromesh."Anal. Chem., 80, 5139-5145 (2008)
  2. S. Hideshima, M. Yanagisawa, A. Arakaki, T. Matsunaga, T. Osaka “Quantitative detection of immunoreaction using magnetite nanoparticles and raman scatterintg spectroscopy."e-J. Surf. Sci. Nanotechnol., 6, 142-146 (2008)
2007
  1. T. Suzuki, Y. Okamura, A. Arakaki, H. Takeyama, T. Matsunaga “Cytoplasmic ATPase involved in ferrous ion uptake from magnetotactic bacterium Magnetospirillum magneticum AMB-1."FEBS Lett., 581, 3443-3448 (2007)
  2. Y. Amemiya, A. Arakaki, S. S. Staniland, T. Tanaka, T. Matsunaga “Controlled formation of magnetite crystal by partial oxidation of ferrous hydroxide in the presence of recombinant magnetotactic bacterial protein mms6."Biomaterials, 28, 5381-5389 (2007)
  3. T. Taguchi, A. Arakaki, H. Takeyama, S. Haraguchi, M. Yoshino, M. Kaneko, Y. Ishimori, T. Matsunaga “Detection of Cryptosporidium parvum oosysts using a microfluidic device equipped with the SUS micromesh and FITC-labeled antibody."Biotechnol. Bioeng., 96, 272-280 (2007)
2006
  1. M. Tanaka, Y. Okamura, A. Arakaki, T. Tanaka, H. Takeyama, T. Matsunaga “Origin of magnetosome membrane: proteomic analysis of magnetosome membrane and comparison with cytoplasmic membrane."Proteomics, 6, 5234-5247 (2006)
2004
  1. A. Arakaki, S. Hideshima, T. Nakagawa, D. Niwa, T. Tanaka, T. Matsunaga, T. Osaka “Detection of biomolecular interaction between biotin and streptavidin on a self-assembled monolayer using magnetic nanoparticles."Biotechnol. Bioeng., 88, 543-546 (2004)
2003
  1. B. Yoza, A. Arakaki, T. Matsunaga “DNA extraction using bacterial magnetic particles modified with hyperbranched polyamidoamime dendrimer."J. Biotechnol., 101, 219-228 (2003)
  2. H. Nakayama, A. Arakaki, K. Maruyama, H. Takeyama, T. Matsunaga “Single-nucleotide polymorphism analysis using fluorescence resonance energy transfer between DNA-labeling fluorophore, fluorescein isothiocyanate, and DNA Intercalator, POPO-3, on bacterial magnetic particles."Biotechnol. Bioeng., 84, 96-102 (2003)
  3. H. Ota, A. Arakaki, T. Tanaka, H. Takeyama, T. Matsunaga “Single nucleotide mismatch analysis using oligonucleotide probes synthesized on bacterial magnetic particle."Biomol. Eng., 20, 305-309 (2003)
  4. B. Yoza, A. Arakaki, K. Maruyama, H. Takeyama, T. Matsunaga “Fully automated DNA extraction from blood using magnetic particles modified with hyperbranched polyamidoamine dendrimer."J. Biosci. Bioeng., 95, 21-26 (2003)
  5. A. Arakaki, J. Webb, T. Matsunaga “A novel protein tightly bound to bacterial magnetic particles in Magnetospirillum magneticum strain AMB-1."J. Biol. Chem., 278, 8745-8750 (2003)
2002
  1. A. Arakaki, H. Takeyama, T. Tanaka, T. Matsunaga “Cadmium recovery by a sulfate-reducing magnetic bacterium, Desulfovibrio magneticums RS-1 using magnetic separation."Appl. Biochem. Biotechnol., 98/100, 833-840 (2002)
  2. T. Sakaguchi, A. Arakaki, T. Matsunaga “Desulfovibrio magnetics sp. nov., a novel sulfate-reducing bacterium that produces intracellular single-domain-sized magnetite particles."Int. J. Syst. Evol. Microbiol., 52, 215-221 (2002)
  3. T. Matsunaga, A. Arakaki, M. Takahoko “Preparation of luciferase bacterial magnetic particle complex by artificial integration of MagA-luciferase fusion protein into the bacterial magnetic particle membrane."Biotechnol. Bioeng., 77, 614-618 (2002)