Biomolecular Engineering Lab., introduction
              in English language
 Apr 19, 2017 updated 

In an effort to contribute to human health and a sustainable society, the Biomolecular Engineering Laboratory is devoted to research and education in fermentation and novel bioprocesses with eukaryotic microbes including Saccharomyces cerevisiae and Aspergillus oryzae, as well as developing high-throughput methods for functional analyses of genes. See the list below to know who we are,  what we  have done and what we are trying.

BEL Research objectives
  • Engineering and  production of proteins for industrial / diagnostic applications
  • Directed evolution
  • Bacterial expression
  • Yeast extracellular production
  • "difficult-to-express" proteins of which industrial applications are promising
  • Receptor proteins
  • Fungal laccases
  • Peptides mimicking bioactive chemical compounds
  • Gene expression regulation and function
    • Molecules involved in chromosomal segregation
    • A quantitative  reporter for yeast assays (fungal secretory beta-galactosidase)
    • Peptide transporters

  • Protein-protein interaction analysis
    • Identifications of interaction domains
    • domain-based  antagonist
BEL Publications
  • see below for detail

Classes (Educational duties in charge)
  • For the 1st year undergrads
    • Guides to Biotechnology/ Bioengineering
    • Guides to Food Sciences (in partial)

  • For the 2nd year undergrads
    • Basic Molecular Biology
    • English in Food Science II

  • For the 3rd year undergrads
    • Genetic Engineering (Techniques in DNA recombination)
    • Exercise : Genetic Engineering
    • Subcloning of a recombinant gene (engineered jellyfish GFP)
For the graduates' course study, we are responsible for
  • Advanced course for Molecular Biology  (which covers advanced technologies used in molecular biology)
  • Technical consultation for gene cloning, plasmid construction and recombinant protein production, etc
separator BEL/LGE History in brief
  • LGE (Lab. Genetic Engineering) Established in 1987 by emeritus professor Keiichi Takeishi
  • Dr. Horie joined (1988).
  • The first seniors  graduated (1991).
  • Dr. Takeishi, elected to Dean (1999-2003).
  • Dr. Takeishi retired (2006).
  • Dr. Kawarasaki joined (2006).
  • LGE 20th anniversary (2007).
  • LGE, reorganized to BEL (2008).
  • Dr. Horie left (2009).
  • Dr. Ito K joined (2010).
  • Dr. Ito K promoted (2016)
  • Dr. Tanaka joined (2017)
BEL  People (at present)
  • Yasuaki Kawarasaki Ph.D.
  • Mizuki Tanaka Ph.D.
  • Visiting researchers from corporations (6)
BEL In-house facilities
  • Thermal cyclers for PCR x4
  • Takara qPCR@x1
  • Shimazu HPLC x1
  • Bioshakers for cultivation x3
  • Cultivation chambers x4
  • Microplate shakers X3
  • Auto-biophotorecorders x4
  • UV/Vis spectrophotometer x1
  • VersaFluor (Fluorometer) x1
  • Microspectrophotometer x1
  • Cell counter x1
  • Microscopes x3
  • UV crosslinker x1
  • Sonicator for cell lysis x1
  • Safety cabinets x2
  • Gel/Image analyzer w/ UV x1
  • Centrifuges (Swing-type, for 96well plates, Angled-type for microtubes x3)
  • Luminometer x1
  • Fridges/Freezers x3
  • Electroporation x2
  • Milli Q (ultrapure-water dispenser)
  • Marubishi Jar-fermentor (2L) w/ cooling unit  x1
  • Luminescent-image capture x1
Shared facilities (available nearby)
  • DNA sequencers
  • Mass spectrometer
  • LC-TOF-MS
  • Conforcal microscope
  • Ultracentrifuge (Hitachi)
  • Benchtop U-centrifuge (Beckman)
  • Cell sorter
  • Lumino/Fluoro imagers
  • Colony picker
  • NMR
  • 96-well plate reader (UV/Vis)
  • Genechip reader
  • Peptide synthesizer
  • BIAcore, etc
separator Weekly Events
  • Reading:  textbooks in English (Essential cell biology)
  • Brief reports on research progresses (every Monday)
  • Journal club (every Friday)
  • Clean up (every Friday)
  • Guest talk (Tuesday, bi-week)
  • TGIF (occasionally, on Friday)
Annual Events and Meetings
  • Jan., ACB  annual symposium
  • Feb., UG 3rds recruiting as cadets
  • Feb., Thesis submission & qualification
  • Mar., Shizuoka Young Scientists' Conference (regional conference)
  • Mar., Graduation/Farewell party
  • Mar., JSBBA annual meeting
  • Apr., Enrollment: "welcome to squadron" party
  • July, short talks about the researches (end of  semester)
  • Sept., Entrance exam. for the graduate course
  • Sept., SBJ annual meeting
  • Oct., JSBBA regional meeting
  • (Research excursion, somewhere in autumn) 
  • Dec., MBSJ annual meeting
  • Dec., Talks about the researches, including summary, introduction, and achievements
  • (Dec., Pacifichem, every 5 yrs)
  • Dec., General cleanup and year-end party
BEL Facebook
https://www.facebook.com /biomolengineerlab?
ref_type=bookmark
(most of the items are written in Japanese language)
Contact Info
Biomolecular Engineering Lab,
School of Food and Nutritional Sciences,
University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan

•Phones
  +81-54-264-5540 (YK)
  +81-54-264-5548 (Lab)

•FAX
  +81-54-264-5540

e-mail address: 
kawarsky(insert atmark here) u-shizuoka-ken.ac.jp


    




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  Lab folks@2016
            JABEE_logo
The research and educational activities in BEL constitute the JABEE program for the School of Food and Nutritional Sciences


Papers published in international journals (reviewed publications)

Hideo Nakano, Tadaaki Tanaka, Yasuaki Kawarasaki and Tsuneo Yamane*: An Increased Rate of Cell-free Protein Synthesis by Condensing Wheat-germ Extract with Ultrafiltration Membranes.  Bioscience, Biotechnology and Biochemistry, 58, 631-634 (1994)

Yasuaki Kawarasaki, Hideo Nakano and Tsuneo Yamane*: Prolonged Cell-free Protein Synthesis in a Batch System Using Wheat Germ Extract. Bioscience, Biotechnology and Biochemistry, 58, 1911-1913 (1994)

 Tsuneo Yamane*, Yasuaki Kawarasaki and Hideo Nakano: In Vitro Protein Biosynthesis Using Ribosome and Foreign mRNA--An Approach to Construct a Protein Biosynthesizer.  Annals of the New York Academy of Sciences, vol. 750, Enzyme Engineering XII, pp146-157 (1995)

Yasuaki Kawarasaki, Takahiro Kawai, Hideo Nakano and Tsuneo Yamane*: A Long-lived Batch Reaction System of Cell-free Protein Synthesis. Analytical Biochemistry, 226, 320-324 (1995)

Hideo Nakano, Tadaaki Tanaka, Yasuaki Kawarasaki and Tsuneo Yamane*: Highly Productive Cell-free Protein Synthesis System Using Condensed Wheat-germ Extract, Journal of Biotechnology, 46, 275-282 (1996)

Yasuaki Kawarasaki, Hideo Nakano and Tsuneo Yamane*: Purification and Some Properties of Wheat Germ Acid Phosphatases, Plant Science, 119, 67-77 (1996).

Hideo Nakano, Yasuaki Kawarasaki and Tsuneo Yamane *: Recent Advances in Cell-free Protein Synthesis towards a Protein Biosynthesizer   Annals of the New York Academy of Sciences, vol. 799 Enzyme Engineering XIII, pp 406-412 (1996)

Yasuaki Kawarasaki, Hideo Nakano, and Tsuneo Yamane*: Phosphatase-immunodepleted Cell-free Protein Synthesis System, Journal of Biotechnology, 61, 199-208 (1998)

Yugo Iwasaki, Tatsuya Nishiyama, Yasuaki Kawarasaki, Hideo Nakano, and Tsuneo Yamane*: Importance of Disulfide Bridge Formation on Folding of Phospholipase D from Streptomyces antibioticus, Journal of Bioscience and Bioengineering, 89, 506-508 (2000)

Yasuaki Kawarasaki*, Satoru Kasahara, Natsuko Kodera, Tomoya Shimbata, Satoshi Sekiguchi, Hideo Nakano, and Tsuneo Yamane: A trimmed viral cap-independent translation enhancing sequence for a rapid in vitro gene expression, Biotechnology Progress., 16, 517-521 (2000)

Yasuaki Kawarasaki*, Yoko Sasaki, Akinori Ikeuchi, Shoji Yamamoto and Tsuneo Yamane: A method for functional mapping of protein-protein binding domain by preferential amplification of the shortest amplicon using PCR, Analytical Biochemistry, 303, 34-41 (2002)

Suang Rungpragayphan, Yasuaki Kawarasaki, Takao Imaeda, Katsunori Kohda, Hideo Nakano and Tsuneo Yamane*: High-throughput, Cloning-independent Protein Library Construction by Combining Single-molecule DNA Amplification with in Vitro Expression, J. Mol. Biol., 318, 395-405 (2002)

Yasuaki Kawarasaki*, Yasuhiro Yamada, Maki Ichimori, Tomoya Shinbata, Katsunori Kohda, Hideo Nakano, Tsuneo Yamane: Stabilization of affinity tagged recombinant protein during/after its expression in cell-free protein synthesis system using wheat-germ extract., J. Biosci. Bioeng., 95, 209-214 (2003)

Akinori Ikeuchi, Yasuaki Kawarasaki*, Tomoya Shinbata, and Tsuneo Yamane: Chimeric Gene Library Construction by a Simple and Highly Versatile Method Using Recombination-Dependent Exponential Amplification. Biotechnol. Progr., 19, 1460-1467 (2003)

Yasuaki Kawarasaki, Karl E. Griswold, James D. Stevenson, Tzvia Selzer, Stephen J. Benkovic, Brent Iverson, and George Georgiou*: Enhanced Crossover SCRATCHY: Construction and High-throughput Screening of a Combinatorial Library Containing Multiple Non-Homologous Crossovers. Nucl. Acid. Res., 31, e126, (2003)

Akinori Ikeuchi, Yoko Sasaki, Yasuaki Kawarasaki*, and Tsuneo Yamane: Exhaustive identification of interaction domains using a high-throughput method based on two-hybrid screening and PCR-convergence: Molecular dissection of a kinetochore subunit Spc34p.  Nucl. Acid. Res., 31, 6953-6962, (2003)

Denfu Chen, Yasuaki Kawarasaki, Hideo Nakano, and Tsuneo Yamane*: Cloning and in vitro and in vivo expressions of plant glutathione S-transferase Zeta class genes. J. Biosci. Bioeng., 95, 594-600 (2003)

Jeong K.J, Kawarasaki Y, Gam J, Harvey BR, Iverson BL, Georgiou G.*: Periplasmic fluorescent reporter protein and its application in high-throughput membrane protein topology analysis. J. Mol. Biol., 341, 901-9 (2004)

Griswold K., Kawarasaki Y., Ghoneim N., Benkovic S., Iverson B.L., and Georgiou G.*: Evolution of Highly Active Enzymes by Homology-Independent Recombination, Proc. Natl. Acad. Sci. USA, 102, 10082-10087 (2005)

Kojima T., Takei Y., Ohtsuka M., Kawarasaki Y., Yamane T., Nakano T.*: PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets., Nucl. Acid. Res. 33, e150 (2005)

Zhao M., Zhou L., Kawarasaki Y., and Georgiou G.*: Regulation of RraA, a protein of RNase E-mediated RNA decay., J. Bacteriol., 188, 3257-3263, (2006)

Tullman-Ercek D., DeLisa M.P., Kawarasaki Y., Iranpour P., Ribnicky B., Palmer T., and Georgiou G*., J. Biol. Chem. 282, 8309-16 (2007)

Kamiya T, Ojima T, Sugimoto K, Nakano H, *Kawarasaki Y. Quantitative Y2H screening: Cloning and signal peptide engineering of a fungal secretory LacA gene and its application to yeast two-hybrid system as a quantitative reporter. J. Biotechnol. 146C151-159, (2010)

Ikeuchi A., Kamiya T., Sugimoto K., Yamane T., Nakano H., and *Kawarasaki Y., A method for reverse interactome analysis: High-resolution mapping of Interdomain interaction network in Dam1 complex and its specific disorganization based on interaction domain expression. Biotech. Progr. 26, 945-953 (2010)

Ito K., *Ito S., Shimamura T., Kawarasaki Y., Abe K., Misaka T., Kobayashi T., and Iwata S., Crystallization and preliminary X-ray analysis of a glucansucrase from the dental caries pathogen Streptococcus mutans. Acta Cryst. F66, 1086-1088 (2010)

Ito K., *Ito S., Shimamura T., Weyand S., Kawarasaki Y., Misaka T., Abe K., Kobayashi T., Cameron A., and Iwata S. Crystal structure of glucansucrase from dental caries pathogen Streptococcus mutans. J. Mol. Biol., 408, 177-186 (2011)

Kojima T, Nagao N, Ando D, Ojima T, Kawarasaki Y, Kobayashi I, Nakajima M, *Nakano H. Emulsion culture: A miniaturized library screening system based on micro-droplets in an emulsified medium. J. Biosci. Bioeng.112, 299-303 (2011)

Kimata K., Yamaguchi M., Saito Y., Hata H., Miyake K., Yamane T., Nakagawa Y., Yano A., Ito K., and *Kawarasaki Y., High cell-density expression system: A novel method for extracellular production of "difficult-to-express" proteins. J. Biosci. Bioeng. 113, 154-159 (2012)

*Ito K, Hikida A, Kitagawa S, Misaka T, Abe K, Kawarasaki Y., Soy Peptides Enhance Heterologous Membrane Protein Productivity during the Exponential Growth Phase of Saccharomyces cerevisiae., Biosci Biotechnol Biochem 76, 628-31 (2012).

Hikida A., *Ito K., Motoyama T., Kato R., Kawarasaki Y.: Systematic analysis of a dipeptide library for inhibitor development using human dipeptidyl peptidase IV produced by a Saccharomyces cerevisiae expression system. Biochem. Biophys. Res. Commun., 430, 1217-22 (2013).

 *Ito K, Hikida A, Kawai S, Lan VTT, Motoyama T, Kitagawa S, Yoshikawa Y, Kato R, Kawarasaki Y.: Analysing the substrate multispecificity of a proton-coupled oligopeptide transporter using a dipeptide library. Nat. Commun., 4:2502 doi: 10.1038/ncomms3502, (2013)

 Kurose T., Saito Y., Kimata K., Nakagawa Y., Yano A., Ito K., and *Kawarasaki Y.: Secretory expression of Lentinula edodes intracellular laccase by yeast high-cell-density system: a sub-milligram production of gdifficult-to-expressh secretory protein. J. Biosci. Bioeng. 117, 659-663 (2014) 10.1016/j.jbiosc.2013.11.014).
 
Lan V.T.T., Ito K., Ohno M., Motoyama T., Ito S., Kawarasaki Y.: Analyzing a dipeptide library to identify human dipeptidyl peptidase IV inhibitor. Food Chem. 175, 66-73 (2015)

Mori A., Hara S., Sugahara T., Kojima T., Iwasaki Y., Kawarasaki Y., Sahara T., Ohgiya S., Nakano H.: Signal peptide optimization tool for the secretion of recombinant protein from Saccharomyces cerevisiae. J Biosci Bioeng. 120, 518-525 (2015)

Ohno M., Ito K., Lan V.T.T, Kusubata M., Tometsuka C., Koyama Y.I., Motoyama T., Ito S., Kawarasaki Y.: Synergistic inhibition of human dipeptidyl peptidase IV by combinations of peptides. Peptides 69, 115-117, (2015)

*Kawarasaki Y., Kurose T., Ito K.: High cell-density expression system: Yeast cells in a phalanx efficiently produce a certain range of gdifficult-to-expressh secretory recombinant proteins, Method. Mol. Biol. 1258, 169-178  gInsoluble Proteins: Methods and Protocolsh Part 9, ed. by Elena Garcia-Fruitos, Humana Press (2015)


Underlined; the BEL lab members
*asterisk; corresponding author


 Biomolecular Engineering Lab  Researchers' Profiles

Yasuaki KAWARASAKI, PhD.,
Assoc. Professor

curriculum vitae

EDUCATION
1992-1997
Graduate School of Agricultural Science, Nagoya University  (PhD)  Agricultural Science
Dissertation: Study of cell-free protein synthesis

1988-1992
School of Agricultural Science, Nagoya University@(Bachelor): Agricultural Chemistry
EMPLOYMENT
2006-present
Associate Professor, University of Shizuoka
  • School of Food and Nutritional Sciences (2006-present)
  • Graduate School of Integrated Pharmaceutical and Nutritional Sciences (2012-present)
  • Graduate School of Nutrition and Environmental Sciences (2006-2012)

2002-2004
Post-doctoral Researcher (Faculty Staff), Dept. Chemical Engineering, University of Texas at Austin

1998-2006
Assistant Professor, Graduate School of Bio and Agricultural Sciences, Nagoya University

1997-1997
Special post-doctoral fellow, Institute of Physical and Chemical Research (RIKEN)

PROFESSIONAL ACTIVITIES
  • Japanese Society for Bioscience and Biotechnology
  • Society for Biotechnology, Japan
  • The molecular biology society of Japan
  • American Chemical Society
  • Association of Combinatorial Bioengineering
  • Japanese Association of Enzyme Engineering
  • Japan Bioindustry Association (JBA)
  • Shizuoka Bioscience Forum for Young Researchers

HONORS/AWARDS
  • Awards for the Excellent Papers 2004, J. Biosci. Bioeng.

KEYWORDS in PRESENT RESEARCHES
  • Biomolecular Engineering based on
    • Directed Evolution
    • Protein Engineering
    • Molecular Biotechnology
  • Gene Expression and Regulation
  • Functional Genomics based on 
    • Interactome Analysis
    • Reverse-proteome analysis based on protein-protein interactions
PUBLICATIONS
See above list.

See also:
Google Schalor's My Citations
http://scholar.google.com/citations?user=rgr_euwAAAAJ

Thomson Reuter's Researcher ID


 Miscellaneous information

Lab Facebook page
http://www.facebook.com/biomolengineerlab

Information for Visitors

Office; Room5410, on the "FOOD" Building 4th floor.
Lab; Room 5409, opposite to the office.

Administration of this webpage;
BEL website committee, chaired by YK
Designed and view-checked with;
SeaMonkey 2.5 for MacOSX
Safari or Firefox for MacOSX
Safari for iPhone

Internal links to our colleagues

External links


Japanese national flag,
            link to the LGE Japanese page
Click to go back to the original@(Japanese) version


Thank you for reading,
- BEL websites subcommittee