Publications

List of Publications:

  1. Shiota M, Yamazaki T, Yoshimatsu K, Kojima K, Tsugawa W, Ferri S, Sode K (2016) An Fe-S cluster in the conserved Cys-rich region in the catalytic subunit of FAD-dependent dehydrogenase complexes. Bioelectrochemistry. Feb 2. pii: S1567-5394(16)30010-X. doi: 10.1016/j.bioelechem.2016.01.010. [Epub ahead of print]
  2. Nakajima M, Abe K, Ferri S, Sode K (2016) Development of a light-regulated cell-recovery system for non-photosynthetic bacteria. Microb Cell Fact. Feb 15;15(1):31.
  3. Ferri S, Nakamura M, Ito A, Nakajima M, Abe K, Kojima K, Sode K (2015) Efficient surface-display of autotransporter proteins in cyanobacteria Algal Research 12: 337–340.
  4.  Fukaya T, Abe K, Savory N, Tsukakoshi K, Yoshida W, Ferri S, Sode K, Ikebukuro K. (2015) Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy. J Biotechnol 212:99-105.
  5. Sakai Y, Abe K, Nakashima S, Ellinger JJ, Ferri S, Sode K, Ikebukuro K. (2015) Scaffold-fused riboregulators for enhanced gene activation in Synechocystis sp. PCC 6803 Microbiologyopen 4(4):533-540.
  6. Badary A, Abe K, Ferri S, Kojima K, Sode K (2015) The development and characterization of an exogenous green-light regulated gene expression system in marine cyanobacteria. Mar Biotechnol (NY). Jun;17(3):245-51.
  7. Kameya M, Sakaguchi-Mikami A, Ferri S, Tsugawa W, Sode K (2015) Advancing the Development of Glycated Protein Biosensing Technology: Next-Generation Sensing Molecules. J Diabetes Sci Technol. Mar;9(2):183-91.
  8. Savory N, Nzakizwanayo J, Abe K, Yoshida W, Ferri S, Dedi C, Jones BV, Ikebukuro K (2014) Selection of DNA aptamers against uropathogenic Escherichia coli NSM59 by quantitative PCR controlled Cell-SELEX. J Microbiol Methods. Sep;104:94-100.
  9. Sakai Y, Abe K, Nakashima S, Yoshida W, Ferri S, Sode K, Ikebukuro K. (2014) Improving the Gene-Regulation Ability of Small RNAs by Scaffold Engineering in Escherichia coli. ACS Synth Biol. Mar 21;3(3):152-62.
  10. Horaguchi Y, Saito S, Kojima K, Tsugawa W, Ferri S, Sode K (2014) Engineering glucose oxidase to minimize the influence of oxygen on sensor response. Electrochimica Acta, Volume 126, issue April 20, p. 158-161.
  11. Miyake K, Abe K, Ferri S, Nakajima M, Nakamura M, Yoshida W, Kojima K, Ikebukuro K, Sode K. (2014) A green-light inducible lytic system for cyanobacterial cells. Biotechnol Biofuels 7(1):56.
  12. Abe K, Miyake K, Nakamura M, Kojima K, Ferri S, Ikebukuro K, Sode K (2014) Engineering of a green-light inducible gene expression system in Synechocystis sp. PCC6803. Microb Biotechnol. Mar;7(2):177-83
  13. Savory N, Takahashi Y, Tsukakoshi K, Hasegawa H, Takase M, Abe K, Yoshida W, Ferri S, Kumazawa S, Sode K, Ikebukuro K (2014) Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans by in silico maturation for biosensor development. Biotechnol Bioeng. Mar;111(3):454-61.
  14. Savory N, Goto S, Yoshida W, Unuma Y, Nakamura M, Abe K, Ferri S, Ikebukuro K (2013) Two-Dimensional Electrophoresis-Based Selection of Aptamers against an Unidentified Protein in a Tissue Sample. Anal Lett. Dec; 46(18):2954-2963
  15. Abe K, Yoshida W, Terada K, Yagi-Ishii Y, Ferri S, Ikebukuro K, Sode K (2013) Screening of peptide ligands for pyrroloquinoline quinone glucose dehydrogenase using antagonistic template-based biopanning. Int J Mol Sci. Nov 25;14(12):23244-56.
  16. Savory N, Lednor D, Tsukakoshi K, Abe K, Yoshida W, Ferri S, Jones BV, Ikebukuro K (2013) In silico maturation of binding-specificity of DNA aptamers against Proteus mirabilis. Biotechnol Bioeng. Oct;110(10):2573-80.
  17. Ferri S, Miyamoto Y, Sakaguchi-Mikami A, Tsugawa W, Sode K (2013) Engineering fructosyl peptide oxidase to improve activity toward the fructosyl hexapeptide standard for HbA1c measurement. Mol Biotechnol. Jul;54(3):939-43.
  18. Sakaguchi-Mikami A, Kameya M, Ferri S, Tsugawa W, Sode K (2013) Cloning and characterization of fructosamine-6-kinase from Arthrobacter aurescens. Appl Biochem Biotechnol. Jun;170(3):710-7.
  19. Yoshida W, Saito T, Yokoyama T, Ferri S, Ikebukuro K (2013) Aptamer selection based on g4-forming promoter region. PLoS One. Jun 4;8(6):e65497.
  20. Sakaguchi-Mikami A, Ferri S, Katayama S, Tsugawa W, Sode K (2013) Identification and functional analysis of fructosyl amino acid-binding protein from Gram-positive bacterium Arthrobacter sp. J Appl Microbiol. May;114(5):1449-56.
  21. Kojima K, Kobayashi T, Tsugawa W, Ferri S, Sode K (2013) Mutational analysis of the oxygen-binding site of cholesterol oxidase and its impact on dye-mediated dehydrogenase activity. J Mol Catal B: Enzym. April 2013, 88: 41–46
  22. Yamashita Y, Ferri S, Huynh ML, Shimizu H, Yamaoka H, Sode K (2013) Direct electron transfer type disposable sensor strip for glucose sensing employing an engineered FAD glucose dehydrogenase. Enzyme Microb Technol. Feb 5;52(2):123-8.
  23. Kojima K, Mikami-Sakaguchi A, Kameya M, Miyamoto Y, Ferri S, Tsugawa W, Sode K (2013) Substrate specificity engineering of Escherichia coli derived fructosamine 6-kinase. Biotechnol Lett. Feb;35(2):253-8.
  24. Nonaka Y, Yoshida W, Abe K, Ferri S, Schulze H, Bachmann TT, Ikebukuro K (2013) Affinity improvement of a VEGF aptamer by in silico maturation for a sensitive VEGF-detection system. Anal Chem. 2013 Jan 15;85(2):1132-7.
  25. Horaguchi Y, Saito S, Kojima K, Tsugawa W, Ferri S, Sode K (2012) Construction of mutant glucose oxidases with increased dye-mediated dehydrogenase activity. Int J Mol Sci. Nov 2;13(11):14149-57.
  26. Ferri S, Sode K (2012) Biomolecular engineering of biosensing molecules – The challenges in creating sensing molecules for glycated protein biosensing. Electrochemistry 80(5):293-298.
  27. Kim S, Nibe E, Tsugawa W, Kojima K, Ferri S, Sode K (2012) Construction of engineered fructosyl peptidyl oxidase for enzyme sensor applications under normal atmospheric conditions. Biotechnol Lett. Mar;34(3):491-7.
  28. Ferri S, Kojima K, Sode K (2011) Review of Glucose Oxidases and Glucose Dehydrogenases: A Bird’s Eye View of Glucose Sensing Enzymes. J Diabetes Sci Technol 5(5):1068-1076.
  29. Mori K, Nakajima M, Kojima K, Murakami K, Ferri S, Sode K (2011) Screening of Aspergillus-derived FAD glucose dehydrogenases from fungal genome database. Biotechnol Lett. 33(11):2255-63.
  30. Ferri S, Nibe E, Miyamoto Y, Kim S, Tsugawa W, Sode K (2011) Tuning Fructosyl Peptidyl Oxidase into Dehydrogenase and Its Application for the Construction of an Enzyme Electrode. ECS Transactions 35(7):113-116.
  31. Kim S, Nibe E, Ferri S, Tsugawa W, Sode K (2010) Engineering of dye-mediated dehydrogenase property of fructosyl amino acid oxidases by site-directed mutagenesis studies of its putative proton relay system. Biotechnol Lett. 32(8):1123-1129.
  32. Kim S, Ferri S, Tsugawa W, Mori K, Sode K (2010) Motif-based search for a novel fructosyl peptide oxidase from genome databases. Biotechnol Bioeng. 106(3):358-366.
  33. Desriani, Ferri S, Sode K (2010) Functional expression of Phanerochaete chrysosporium cellobiose dehydrogenase flavin domain in Escherichia coli. Biotechnol. Lett. 32(6):855-859.
  34. Desriani, Ferri S, Sode K (2010) Amino acid substitution at the substrate-binding subsite alters the specificity of the Phanerochaete chrysosporium cellobiose dehydrogenase. Biochem. Biophys. Res. Com. 391(2): 1246-1250
  35. Ferri S, Kim S, Tsugawa W, Sode K (2009) Review of Fructosyl Amino Acid Oxidase Engineering Research: A Glimpse into the Future of Hemoglobin A1c Biosensing. J Diabetes Sci Technol 3(3):585-592.
  36. Hanashi T, Yamazaki T, Tsugawa W, Ferri S, Nakayama D, Tomiyama M, Ikebukuro K, Sode K (2009) BioCapacitor – a novel category of biosensor. Biosens Bioelectron. Mar 15;24(7):1837-42.
  37. Kim S, Miura S, Ferri S, Tsugawa W, Sode K (2009) Cumulative effect of amino acid substitution at the putative active site of fructosyl amine oxidase. Enzyme and Microbial Technology 44: 52–56.
  38. Yamaoka H, Yamashita Y, Ferri S, Sode K. (2008) Site directed mutagenesis studies of FAD-dependent glucose dehydrogenase catalytic subunit of Burkholderia cepacia. Biotechnol Lett. 30(11):1967-72.
  39. Sakaguchi-Mikami A, Taneoka A, Yamoto R, Ferri S, Sode K (2008) Engineering of Ligand Specificity of Periplasmic Binding Protein for Glucose Sensing. Biotechnol. Lett. 30(8):1453-60
  40. Miura S, Ferri S, Tsugawa W, Kim S, Sode K (2008) Development of fructosyl amine oxidase specific to fructosyl valine by site-directed mutagenesis. Protein Eng Des Sel. 21: 233-239
  41. Chino S, Sakaguchi A, Yamoto R, Ferri S, Sode K (2007) Branched-chain Amino Acid Biosensing Using Fluorescent Modified Engineered Leucine/Isoleucine/Valine Binding Protein. Int J Mol Sci. 8: 513-525.
  42. Sakaguchi A, Ferri S, Tsugawa W, Sode K (2007) Novel fluorescent nanosensor for a-fructosyl amino acids based on engineered fructosyl amino acid binding protein. Biosens Bioelectron 22(9-10):1933-8.
  43. Miura S, Ferri S, Tsugawa W, Kim S, Sode K (2006) Active site analysis of fructosyl amine oxidase using homology modeling and site-directed mutagenesis. Biotechnol. Lett. 23:1895-900.
  44. Tsuya T, Ferri S, Fujikawa M, Yamaoka H, Sode K (2006) Cloning and functional expression of glucose dehydrogenase complex of Burkholderia cepacia in Escherichia coli. J. Biotechnol. 123 (2), 127–136.
  45. Sakaguchi A, Ferri S, Sode K (2005) SocA is a novel periplasmic binding protein for fructosyl amino acid. Biochem. Biophys. Res. Com. 336(4):1074-1080.
  46. Tanaka S, Igarashi S, Ferri S, Sode K (2005) Increasing stability of water-soluble PQQ glucose dehydrogenase by increasing hydrophobic interaction at dimeric interface. BMC Biochemistry. 6; 1.
  47. Ferri S, Sakaguchi A, Goto H, Tsugawa W, Sode K (2005) Isolation and Characterization of a Fructosyl-amine Oxidase from Arthrobacter Sp FV1-1. Biotechnol. Lett. 27(1):27-32.
  48. Ferri S, Miura S, Sakaguchi A, Ishimura F, Tsugawa W, and Sode K (2004) Cloning and Expression of a Fructosyl-amine Oxidase from the Marine Yeast Pichia Sp N1-1. Mar Biotechnol (NY) 6(6):625-32.
  49. Yamaoka H, Ferri S, Fujikawa M, Sode K (2004) Essential role of the small subunit of thermostable glucose dehydrogenase from Burkholderia cepacia. Biotechnol. Lett. 26(22):1757-61.
  50. Tamada T, Feese MD, Ferri SR, Kato Y, Yajima R, Toguri T, Kuroki R (2004) Substrate recognition and selectivity of plant glycerol-3-phosphate acyltransferases (GPATs) from Cucurbita moscata and Spinacea oleracea. Acta Cryst. D60, 13-21.
  51. Sakaguchi A, Tsugawa W, Ferri S, Sode K (2003) Development of a highly sensitive fructosyl-valine enzyme sensor employing recombinant fructosyl amine oxidase. Electrochemistry 76(6): 442-445.
  52. Ogawa K, Stöllner D, Scheller F, Warsinke A, Ishimura F, Tsugawa W, Ferri S, Sode K (2002) Development of a flow injection analysis (FIA) enzyme sensor for fructosyl amine monitoring. Anal. Bioanal. Chem. 373: 211-214.
  53. Tamada T, Ferri SR, Toguri T, Kuroki R (2001) Structure and Function of Glycerol-3-Phosphate Acyltransferase. The Journal of Structural Biology SAKABE Project 7(3) 1-10 [Japanese]
  54. Ferri SR, Toguri T (1997) Substrate Specificity Modification of the Stromal Glycerol-3-phosphate Acyltransferase. Arch. Biochem. Biophys. 337(2):202-208.
  55. Ferri SR, Oshizaki-Nishizawa O, Azuma M, Toguri T (1997) Identification of a Region in Stromal Glycerol 3-phosphate Acyltransferase which Controls Acyl Chain Specificity. in Physiology, Biochemistry and Molecular Biology of Plant Lipids (Williams JP, Khan MU, Lem NW, eds.) pp. 137-139, Kluwer Academic Publishers, Netherlands.
  56. Lawson DM, Derewenda U, Serre L, Ferri S, Szittner R, Wei Y, Meighen EA, Derewenda ZS (1994) Structure of a Myristoyl-ACP-specific Thioesterase from Vibrio harveyi. Biochemistry. 33(32): 9382-8.
  57. Ferri SR, Meighen EA (1994) An Essential Histidine Residue Required for Fatty Acylation and Acyl Transfer by Myristoyltransferase from Luminescent Bacteria. J. Biol. Chem. 269(9):6683-8.
  58. Swenson L, Ferri SR, Green R, Sharp AM, Meighen EA, Derewenda ZS (1992) Expression, Purification and Crystallization of the Vibrio harveyi Acyltransferase. J. Mol. Biol. 227(2):572-4.
  59. Ferri SR, Meighen EA (1991) A Lux-specific Myristoyl Transferase in Luminescent Bacteria Related to Eukaryotic Serine Esterases. J. Biol. Chem. 266(20):12852-12857.
  60. Ferri S, Soly RR, Miyamoto C, Meighen E (1991) Complementation In Vivo of the Lux-specific Fatty Acid Reductase Subunits from Different Luminescent Bacteria. in Bioluminescence and Chemiluminescence: Current Status (PE Stanley & LJ Kricka, eds.) pp. 39-42, John Wiley & Sons.
  61. Ferri SR, Soly RR, Szittner RB, Meighen EA (1991) Structure and Properties of Luciferase from Photobacterium phosphoreum. Biochem. Biophys. Res. Com. 176(1):541-548.
  62. Mancini J, Boylan M, Soly R, Ferri S, Szittner R, Meighen E (1989) Organization of the Lux Genes of Photobacterium phosphoreum. J. Biolumin. Chemilumin. 3: 201-205.
  63. Soly RR, Mancini JA, Ferri SR, Boylan M, Meighen EA (1988) A New Lux Gene in Bioluminescent Bacteria Codes for a Protein Homologous to the Bacterial Luciferase Subunits. Biochem. Biophys. Res. Com. 155(1): 351-358.

 

Patents:

Ferri SR and Toguri T (Kirin Brewery Co., Ltd.) DNA Strands Encoding Glycerol-3-Phosphate Acyltransferase. Patent filed in 1995: JP19950192123 (US6160203, EP0843007, WO9705246).

Ferri SR and Toguri T (Kirin Brewery Co., Ltd.) β-ketoacyl-ACP Synthase II enzymes and genes coding for same. Patent filed in 1997: JP19970011430 (US6200788, EP0969014, WO9832770).

 

Invited Lectures:

Ferri S (2011) The International Genetically Engineered Machine Competition – an overview of iGEM. 酵素工学研究会 第66 回講演会 (invited lecture) Sept., Tokyo.

Ferri S (2011) The iGEM Jamboree – a great addition to a science student’s training. 第63 回日本生物工学会大会 (invited lecture) Sept., Tokyo.