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Perspective

Finding and defining the natural automata acting in living plants: Toward the synthetic biology for robotics and informatics in vivo

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Pages 519-526 | Published online: 01 Nov 2012

References

  • Kari L. The many facets of natural computing. Commun ACM 2008; 51:72 - 83; http://dx.doi.org/10.1145/1400181.1400200
  • Tomita Y, Yokomori T. Automata and formal language. 1992; Morikita Publ. Tokyo.
  • Amos M. Genesis machines. New science of biocomputing. Atlantic Books 2006; London.
  • Andrianantoandro E, Basu S, Karig DK, Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2006; 2:2006 - , 0028; http://dx.doi.org/10.1038/msb4100073; PMID: 16738572
  • Kurihara K, Tamura M, Shohda K, Toyota T, Suzuki K, Sugawara T. Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA. Nat Chem 2011; 3:775 - 81; http://dx.doi.org/10.1038/nchem.1127; PMID: 21941249
  • Nandagopal N, Elowitz MB. Synthetic biology: integrated gene circuits. Science 2011; 333:1244 - 8; http://dx.doi.org/10.1126/science.1207084; PMID: 21885772
  • Canton B, Labno A, Endy D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 2008; 26:787 - 93; http://dx.doi.org/10.1038/nbt1413; PMID: 18612302
  • Brown J. The iGEM competition: building with biology. Synth Biol 2007; 1:3 - 6; http://dx.doi.org/10.1049/iet-stb:20079020
  • Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin AP, et al. BglBricks: A flexible standard for biological part assembly. J Biol Eng 2010; 4:1; http://dx.doi.org/10.1186/1754-1611-4-1; PMID: 20205762
  • Benenson Y. Biocomputers: from test tubes to live cells. Mol Biosyst 2009; 5:675 - 85; http://dx.doi.org/10.1039/b902484k; PMID: 19562106
  • Benenson Y. Biocomputing: DNA computes a square root. Nat Nanotechnol 2011; 6:465 - 7; http://dx.doi.org/10.1038/nnano.2011.128; PMID: 21814231
  • Mealy GH. Method for synthesizing sequential circuits. Bell Syst Tech J 1955; 34:1045 - 79
  • Moore EF. Tgedanken-experiments on sequential machines. In: Automata studies. Princeton Univ. Press, Princeton, USA. 1956; pp. 129-153.
  • Volkov AG, Adesina T, Markin VS, Jovanov E. Kinetics and mechanism of Dionaea muscipula trap closing. Plant Physiol 2008; 146:694 - 702; http://dx.doi.org/10.1104/pp.107.108241; PMID: 18065564
  • Ueda M, Nakamura Y, Okada M. Endogenous factors involved in the regulation of movement and” memory” in plants. Pure Appl Chem 2007; 79:519 - 27; http://dx.doi.org/10.1351/pac200779040519
  • Li Y, Zhang M. Nonlinear dynamics in the trapping movement of the Venus flytrap. Proc. Am Control Conf. 2011; pp. 3514-351.
  • Volkov AG, Adesina T, Jovanov E. Closing of venus flytrap by electrical stimulation of motor cells. Plant Signal Behav 2007; 2:139 - 45; http://dx.doi.org/10.4161/psb.2.3.4217; PMID: 19516982
  • Yoshioka H, Bouteau F, Kawano T. Discovery of oxidative burst in the field of plant immunity: Looking back at the early pioneering works and towards the future development. Plant Signal Behav 2008; 3:153 - 5; http://dx.doi.org/10.4161/psb.3.3.5537; PMID: 19513209
  • Passardi F, Cosio C, Penel C, Dunand C. Peroxidases have more functions than a Swiss army knife. Plant Cell Rep 2005; 24:255 - 65; http://dx.doi.org/10.1007/s00299-005-0972-6; PMID: 15856234
  • Kawano T. Roles of the reactive oxygen species-generating peroxidase reactions in plant defense and growth induction. Plant Cell Rep 2003; 21:829 - 37; PMID: 12789499
  • Kawano T, Sahashi N, Takahashi K, Uozumi N, Muto S. Salicylic acid induces extracellular superoxide generation followed by an increase in cytosolic calcium ion in tobacco suspension culture. The earliest events in salicylic acid signal transduction. Plant Cell Physiol 1998; 39:721 - 30; http://dx.doi.org/10.1093/oxfordjournals.pcp.a029426
  • Kawano T, Muto S. Mechanism of peroxidase actions for salicylic acid-induced generation of active oxygen species and an increase in cytosolic calcium in tobacco cell suspension culture. J Exp Bot 2000; 51:685 - 93; http://dx.doi.org/10.1093/jexbot/51.345.685; PMID: 10938860
  • Kawano T, Muto S, Adachi M, Hosoya H, Lapeyrie F. Spectroscopic evidence in support of horseradish peroxidase compound II-catalyzed oxidation of salicylic acid but not of phenylethylamine. Biosci Biotechnol Biochem 2002; 66:651 - 4; http://dx.doi.org/10.1271/bbb.66.651; PMID: 12005064
  • Kawano T, Muto S, Adachi M, Hosoya H, Lapeyrie F. Spectroscopic evidence that salicylic acid converts a temporally inactivated form of horseradish peroxidase (compound III) to the irreversibly inactivated verdohemoprotein (P-670). Biosci Biotechnol Biochem 2002; 66:646 - 50; http://dx.doi.org/10.1271/bbb.66.646; PMID: 12005063
  • Kawano T, Pinontoan R, Uozumi N, Miyake C, Asada K, Kolattukudy PE, et al. Aromatic monoamine-induced immediate oxidative burst leading to an increase in cytosolic Ca2+ concentration in tobacco suspension culture. Plant Cell Physiol 2000; 41:1251 - 8; http://dx.doi.org/10.1093/pcp/pcd052; PMID: 11092910
  • Kawano T, Pinontoan R, Uozumi N, Morimitsu Y, Miyake C, Asada K, et al. Phenylethylamine-induced generation of reactive oxygen species and ascorbate free radicals in tobacco suspension culture: mechanism for oxidative burst mediating Ca2+ influx. Plant Cell Physiol 2000; 41:1259 - 66; http://dx.doi.org/10.1093/pcp/pcd053; PMID: 11092911
  • Rutter R, Valentine M, Hendrich MP, Hager LP, Debrunner PG. Chemical nature of the porphyrin pi cation radical in horseradish peroxidase compound I. Biochemistry 1983; 22:4769 - 74; http://dx.doi.org/10.1021/bi00289a024; PMID: 6313048
  • Schulz CE, Rutter R, Sage JT, Debrunner PG, Hager LP. Mössbauer and electron paramagnetic resonance studies of horseradish peroxidase and its catalytic intermediates. Biochemistry 1984; 23:4743 - 54; http://dx.doi.org/10.1021/bi00315a033; PMID: 6093863
  • Kawano T, Pinontoan R, Hosoya H, Muto S. Monoamine-dependent production of reactive oxygen species catalyzed by pseudoperoxidase activity of human hemoglobin. Biosci Biotechnol Biochem 2002; 66:1224 - 32; http://dx.doi.org/10.1271/bbb.66.1224; PMID: 12162542
  • Gazaryan IG, Lagrimini LM, Ashby GA, Thorneley RN. Mechanism of indole-3-acetic acid oxidation by plant peroxidases: anaerobic stopped-flow spectrophotometric studies on horseradish and tobacco peroxidases. Biochem J 1996; 313:841 - 7; PMID: 8611164
  • Savitsky PA, Gazaryan IG, Tishkov VI, Lagrimini LM, Ruzgas T, Gorton L. Oxidation of indole-3-acetic acid by dioxygen catalysed by plant peroxidases: specificity for the enzyme structure. Biochem J 1999; 340:579 - 83; http://dx.doi.org/10.1042/0264-6021:3400579; PMID: 10359640
  • Kawano T, Kawano N, Hosoya H, Lapeyrie F. Fungal auxin antagonist hypaphorine competitively inhibits indole-3-acetic acid-dependent superoxide generation by horseradish peroxidase. Biochem Biophys Res Commun 2001; 288:546 - 51; http://dx.doi.org/10.1006/bbrc.2001.5800; PMID: 11676477
  • Kawano T, Kawano N, Lapeyrie F. A fungal auxin antagonist, hypaphorine prevents the indole-3-acetic acid-dependent irreversible inactivation of horseradish peroxidase: inhibition of Compound III-mediated formation of P-670. Biochem Biophys Res Commun 2002; 294:553 - 9; http://dx.doi.org/10.1016/S0006-291X(02)00513-2; PMID: 12056802
  • Kawano T, Furuichi T, Muto S. Controlled free salicylic acid levels and corresponding signaling mechanisms in plants. Plant Biotechnol 2004; 21:319 - 35; http://dx.doi.org/10.5511/plantbiotechnology.21.319
  • Takayama A, Kadono T, Kawano T. Heme redox cycling in soybean peroxidase: Hypothetical model and supportive data. Sens. Mater. 2012; 24:87 - 97
  • Mazzolai B, Laschi C, Dario P, Mugnai S, Mancuso S. The plant as a biomechatronic system. Plant Signal Behav 2010; 5:90 - 3; http://dx.doi.org/10.4161/psb.5.2.10457; PMID: 20023403
  • Mancuso S. The roots of plant intelligence. 2010; http://www.ted.com/talks/stefano_mancuso_the_roots_of_plant_intelligence.html.
  • Kagenishi T, Yokawa K, Kadono T, Uezu K, Kawano T. Copper-binding peptides from human prion protein and newly designed peroxidative biocatalysts. Z Naturforsch C 2011; 66:182 - 90; http://dx.doi.org/10.5560/ZNC.2011.66c0182; PMID: 21630593
  • Miyoshi N, Kawano T, Tanaka M, Kadono T, Kosaka T, Kunimoto M, et al. Use of Paramecium species in bioassays for environmental risk management: determination of IC50 values for water pollutants. J Health Sci 2003; 46:429 - 35; http://dx.doi.org/10.1248/jhs.49.429
  • Pech LL. Regulation of ciliary motility in Paramecium by cAMP and cGMP. Comp Biochem Physiol A 1995; 111:31 - 7; http://dx.doi.org/10.1016/0300-9629(95)98516-J
  • Machemer H, de Peyer JE. Swimming sensory cells: electrical membrane parameters, receptor properties and motor control in ciliated protozoa. Verh. Deutsche Zool Gesellschaft, Erlangen, 1977; pp. 86-110.
  • Naitoh Y. Protozoa. In: Electrical Conduction and Behaviour in “Simple” Invertebrates, Ed. Shelton G.A.B., Clarendon Press, Oxford, 1982; pp. 1-48.
  • Aonuma M, Kadono T, Kawano T. Inhibition of anodic galvanotaxis of green paramecia by T-type calcium channel inhibitors. Z Naturforsch C 2007; 62:93 - 102; PMID: 17425113
  • Ludloff K. Untersuchungen uber den Galvanotropismus. Arch Gesamte Physiol 1895; 59:525 - 54; http://dx.doi.org/10.1007/BF01789963
  • Itoh A. Motion control of protozoa for Bio MEMS. IEEE/ASME Trans Mechatron 2000; 5:181 - 8; http://dx.doi.org/10.1109/3516.847091
  • Ogawa N, Oku H, Hashimoto K, Ishikawa M. Motile cell galvanotaxis control using high-speed tracking system. Proc IEEE Int Conf Robotics Automation 2004; pp. 1646-51.
  • Ogawa N, Oku H, Hashimoto K, Ishikawa M. Dynamics model of paramecium galvanotaxis for microrobotic application. Proc IEEE Int Conf Robotics Automation 2005; pp. 1258-63.
  • Furukawa S, Karaki C, Kawano T. Micro-particle transporting system using galvanotactically stimulated apo-symbiotic cells of Paramecium bursaria.. Z Naturforsch C 2009; 64:421 - 33; PMID: 19678550
  • Furukawa S, Kawano T. Enhanced microsphere transport in capillary by conditioned cells of green paramecia used as living micromachines controlled under electric stimuli. Sens Mater 2012;24:375-86