1. Development of the High-speed Molecular Evolution
System for Enzymes using Nanobiochip Technologies.
This 5 years (2009~2013) project aims to establish innovative manufacturing
molecular machines based on nanobioscience under CREST program of Japan Science
Object: To develop a chip-based system platform to perform the directed
evolution (i.e., the generation of genetic diversity followed by selection of
improved functional variant) on a chip which reduces cost, time with several
order of magnitudes and increase precision over conventional off chip-based
system. This project is targeted to improve the catalytic activity of cellulase
(an enzyme to convert biomass into fermentable sugars) for cost-effective
biofuel production. Final goal of this project to realize a practical and
versatile system for the evolution of enzyme molecule that are useful in various
application fields including medicines, diagnosis, food processing, bioenergy,
Project director: Prof Takanori Ichiki, The University of Tokyo Collaborators:
Prof Takashi Funatsu (The University of Tokyo), Prof Naoto Nemoto (Saitama
University), and Nikon instrumentation group
2. On-chip cell analysis of cancer preventive
phytochemicals in Indian herbal plant extracts.
This 2 years (2010~2012) bilateral project between India (Biyani College,
University of Rajasthan) and Japan (University of Tokyo) aims to discover
chemopreventive drugs (phytochemicals) for cancer under India-Japan Cooperative
Science Program funded by DST (India) and JSPS (Japan).
Object: The object of this research project is to develop a high-throughput
on-chip based platform for molecular mechanism-based analysis and evaluating
chemopreventive effects of a wide array of phytochemicals derived from various
Indian herbal plant extracts. To accomplish this and as shown below, first a
high-throughput electrical and optical measurement system using on-chip
micorcapillary electrophoresis and FUCCI (fluorescent ubiqutination-based cell
cycle indicator) will be developed and optimized for analysing the effects of
phytochemicals on cancer cells (Japanese side). On the other side, various plant
extracts will be prepared and studied in its crude from on the chemopreventive
action in mice as animal model followed by isolation of active phytochemicals
(Indian side). Finally, new combination with improved action of phytochemicals
will be evaluated against cancer by experiment-exchange training programs for
young researchers of both countries.
Collaborators: Prof Takanori Ichiki, Prof Takanori Akagi (The University of
Tokyo), Prof Ashok Kumar (University of Rajasthan).
3. On-line database development for genotyping
diagnostics for fungal plant pathogens.
This bilateral project is committed to the principles of open research with a
mutual interest between India (Biyani College, University of Rajasthan) and
Japan (Nishigaki Lab, Saitama University) since its inception in 2009 and is
funded by internal resources of each counter-part institutes.
Object: This project is aimed first, to build a molecular database and a
convenient on-line method for rapid identification of plant pathogens and
second, to develop a comprehensive cyber-infrastructure and computer-based
environment that enables distributed teams of molecular bio-researchers to
collaborate and leverage their work by cataloging and integrating available data
into a format that can be easily shared and maximally utilized. To demonstrate
this, near one hundred fungi pathogenic species from different fields in India
will be used to archive Genome Profiling (GP)-based fungal database format.
Collaborators: Prof Koichi Nishigaki (Saitama University), Prof P.C. Trivedi
(University of Rajasthan).
4. Directed evolution and screening of translation
enhancer sequences (5’UTR) for improved protein synthesis in cell-free
This project is committed to the principles of open research with a mutual
interest between India (Biyani College) and Japan (Shimadzu Biotech and Saitama
University) since its inception in 2007 and is funded by internal resources of
Object: Cell-free translation systems have become an important and convenient
tool for proteomic analyses but low functional protein yields obtained using an
exogenous mRNA template due to low translational efficiency is the biggest
problem in the use of cell-free translation systems. This project aims to
develop a novel strategy for the in vitro selection of strong translation
enhancer sequences for use in any given cell-free translation system using mRNA
Collaborators: Dr Masamitsu Shikata (Shimadzu Corp.), Prof Naoto Nemoto (Saitama
5. Development of Bio-ID briefcase and Bio-ID chip for home health monitoring.
This bilateral project between India and Japan is committed to the principles of open research since its inception in 2011 and is funded by internal resources. This project is aimed to establish a molecular surveillance system for home health monitoring and to develop an ‘all-in-one’ molecular diagnostic chip for on-line and in-house detection of malaria-causing plasmodium species and their resistance to multiple malarial drugs. This system will fulfill the ASSURED criteria: Affordable (<$3 per running sample), Sensitive (single-base difference), Specific (gene-level), User friendly (in-house application), Rapid and robust (<30 min), Equipment-free (portable-to-microchip) and Delivered to those who need it (on-line).
6. On-chip Protein phosphorylation for global identification of bona fide substrates of protein kinase.
Collaborators: SMS Medical College, Saitama U, Akita Prefectural U, Lifetech Co. Ltd.
This trilateral project between India, Japan and UK is committed to the principles of open research since its inception in 2010 and is funded by internal resources. This project is aimed to develop a new array platform for global identification of bona fide substrates of protein kinase and analysis of on-chip protein phosphorylation.
7. Directed enzyme evolution of Lin genes for the improved degradation and detoxification of Hexachlorocyclohexance (HCH) and their application in field-scale bioremediation.
Collaborators: Prof Nancy Papalopulu (University of Manchester), Prof Takanori Ichiki (The University of Tokyo), Prof Tsunehiko Higuchi (Nagoya City University).
This project is aimed to screen a variant of Lin genes (superior biological enzyme) for the improved degradation and detoxification of Hexachlorocyclohexance (HCH) and their application in field-scale bioremediation.
8. In vitro selection of peptide aptamer to inhibit misfolded SOD1 aggregation and their drug application in Motor Neuron Disease (ALS).
Collaborators: Prof Rup Lal (University of Delhi), Prof Takanori Ichiki (The University of Tokyo).
This bilateral project between India and Japan is aimed to screen peptide aptamer to inhibit misfolded SOD1 aggregation and their drug application to cure Motor Neuron Disease.
8. G-quadruplex-conjugated multi-dimensional self-assembly growth for bionanoarchitectures.
Collaborators: Dr Koji Yamanaka (Brain Science Institute, RIKEN), Prof Koichi Nishigaki (Saitama University), Dr Koichiro Kitamura (Janusys Corporation).
Collaborators: Prof Koichi Nishigaki (Saitama University), Prof Yoshifumi Nishimura (Yokohama City University), Dr Masahiro Fujita (RIKEN)
..:: Accomplished Research
1. Saitama-Bio project
This 5 years (2003~2007) project aimed to apply evolutionary molecular
engineering to advanced bio-industries under CREATE program of Japan Science &
Technology and titled as REDS (Rational Evolutionary Design of Advanced
Project director: Prof Yuzuru Husimi
Project collaborators: [Industry] Chiome Bioscience Inc., Katakura Industries Co.Ltd., Taisho Pharmaceutical Co.Ltd., Asubio
Pharmaceuticals Inc., Janusys Corporation, Lifetech Co.Ltd., Enplas Corporation.
[Academia] Saitama University, RIKEN, The University of Tokyo, Kyushu
University, Niigata University, Toyohashi University of Technology, Ochanomizu
University. [Government] Saitama Cancer Center, Saitama Industrial Technology
Project Achievements: [Equipment developed] Universal high speed evolution
reactor process, Microbiology analytical devices, Miniature SPR bio sensor,
Simple analytical system for genome variations. [High-functional biomolecules
created] New high function antibodies, New high function peptides, Cancer
related functional molecules, Cell differentiation factors, Harmful chemical
substance non toxic bacterial drugs. [3 venture companies established] (1)
Development of antibody medicines using Japan’s proprietary, new AdLib method
from Chiome Bioscience, Inc. (2) Diagnostic reagents and therapeutic drugs from
peptides (protein) of JANUSYS corporation and (3) Energy and reduced sludge from
new wastewater treatment system of Clarus Environment, Co., Ltd.