National Institute for Basic Biology


Head of Facility:
Takashi Horiuchi (April 1, 1996 -)
Associate Professor:
Masakatsu Watanabe
Research Associates:
Yoshio Hamada, (Tissue and Cell Culture)
Atsushi Ogiwara (Computer)
NIBB Fellow:
Mineo Iseki (Large Spectrograph)
Technical Staffs:
Masayo Iwaki
Mamoru Kubota
Chieko Nanba
Toshiki Ohkawa
Kaoru Sawada
Tomoki Miwa
Hideko Nonaka (- April 30, 1996)

The Facility provides large-and medium-scale instruments and facilities for biophysical, molecular biological, and computational analyses as well as for growing and maintaining biological specimens. The facility is shared among the research members, and has seven laboratories, among which the Large Spectrograph Laboratory and the Laboratory of Stress-Resistant Plants are dedicated to cooperative use under the NIBB Cooperative Research Programs.

On Nov. 12-14, 1996, the Research Support Facility organized an international symposium at NIBB on "New Prospects of Photobiology and the Future Plan of the Okazaki Large Spectrograph" participated by about 40 foreign and about 120 Japanese active scientists, and then got an overwhelming support for the idea of constructing a new generation spectrograph (Okazaki Super Sectrograph) providing about 2 orders of magnitude higher fluence rates (intensities) and versatile combinations of monochromatic irradiations by the use of over 50 tunable laser systems as the major light sources.

I. Facilities

1. The Large Spectrograph Laboratory

This laboratory provides, for cooperative use, the Okazaki Large Spectrograph (OLS), which is the largest spectrograph in the world, dedicated to action spectroscopical studies of various light-controlled biological processes. The spectrograph runs on a 30 kW-Xenon arc lamp and has a compound grating composed of 36 smaller individual gratings. It projects a spectrum of a wavelength range from 250 nm (ultraviolet) to 1,000 nm (infrared) onto its focal curve of 10 m in length. The fluence rate (intensity) of the monochromatic light at each wavelength is more than twice as much as that of the corresponding monochromatic component of tropial sunlight at noon (Watanabe et al., 1982, Photochem. Photobiol., 36, 491-498).

A tunable two-wavelength CW laser irradiation system is also available as a complementary light source to OLS to be used in irradiation experiments which specifically require ultra-high fluence rates as well as ultra-high spectral-, time-and spatial resolutions. It is composed of a high-power Ar-ion laser (Coherent, Innova 20) (336.6-528.7 nm, 20 W output), two CW dye lasers (Coherent, CR599-01) (420-930 nm, 250-1000 mW output), A/O modulators (up to 40 MHz) to chop the laser beam, a beam expander, and a tracking microbeam irradiator (up to 200 mm s-1 in tracking speed, down to 2 mm in beam diameter) with an infrared phase-contrast observation system.

2. Tissue and Cell Culture Laboratory

Various equipments for tissue and cell culture are provided. This laboratory is equipped with safely rooms which satisfy the P2/P3 physical containment level. This facility is routinely used for DNA recombination experiments.

3. Computer Laboratory

To meet various computational needs and to provide means of electronic communication in this institute, many kind of computers are equipped: UNIX servers and engineering workstations (SPARCstations, IRIS machines, NEWS machines, etc.), VAX mini computer system, and some personal computers (Macintosh's and Windows machines). All of these machines are connected each other with local area networks, which are also linked to the high performance multimedia backbone network of Okazaki National Research Institutes. Since this backbone network, called ORION, is joined to the Internet, the users can access various services and databases on the Internet.

The Computer Laboratory provides various computational services to the institute members: file servers for Macintosh and NetWare users, print servers for PC and UNIX users, computational servers that provides sequence analyses and database retrievals, communication servers to the Internet, and so on.

A new computational server with large scale disk system was introduced at the end of this year and started to provide database search service. The laboratory also provides an information dispatching service to the Internet using the World Wide Web (WWW; URL is

4. Plant Culture Laboratory

There are a large number of culture boxes, and a limited number of rooms with environmental control for plant culture. In some of these facilities and rooms, experiments can be carried out at the P1 physical containment level.

5. Experimental Farm

This laboratory consists of two 20 m2 glass-houses with precise temperature and humidity control, a small farm, two greenhouses (45 and 88 m2) with automatic sprinklers, two open aquariums (30 and 50 t) and several smaller tanks. The laboratory also includes a building with office, storage and work-space.

6. Plant Cell Laboratory

Autotrophic and heterotrophic culture devices and are equipped for experimental cultures of plant and microbial cells. A facility for preparation of plant cell cultures including an aseptic room with clean-benches, is also provided.

7. Laboratory of Stress-Resistant Plants

This laboratory was founded to study transgenic plants with respect to tolerance toward various environmental stresses. It is located in the Agricultural Experimental Station of Nagoya University (30 km from the National Institute for Basic Biology). The laboratory provides a variety of growth chambers that precisely control the conditions of plant growth and facilities for molecular biological, and physiological evaluations of transgenic plants.

The laboratory is also a base of domestic and international collaborations devoted to the topic of stress-resistant transgenic plants.

II. Research activities

1. Faculty

The faculty of the Research Support Facility conducts its own research as well as scientific and administrative public services.

(1) Photobiology: Photoreceptive and signal trans-duction mechanisms of phototaxis of single-celled, flagellate algae are studied action spectroscopically (Watanabe 1995, In CRC Handbook of Organic Photochemistry and Photobiology) by measuring computerized-videomiceographs of the motile behavior of the cells at the cellular and subcellular levels (Erata et al. 1995, Protoplasma). Photo-receptive and signal tranduction mechanisms of algal gametogenesis are also studied by action spectroscopy.

(2) Developmental Biology: Notch is an integral cell surface membrane protein that is known to play a key role in developmental cell-cell interactions in Drosophila, particularly in lateral specification of neural versus epidermal cell fates, a process described thus far only in invertebrates. It is thought to act by a direct signaling pathway rather than through one of the classical signal transduction cascades. The mammalian genome is known to contain three Notch homologues but their developmental significance is not clear. To investigate their role in mammalian development, we have sequenced the murine Notch 2 cDNA, determined the primary sequence of its protein, and have investigated its genomic organization. We are now attempting to produce a mutant in which the ankyrin repeat region of Notch 2 is replaced by lacZ. Analysis of the mutant phenotype will provide us with insights about the significance of the repeat in Notch 2 signal transduction in relation to its developmental importance.

(3) Computational Biology: One of the main theme of computational biology is to predict biological functions from amino acids or nucleic acids sequences. Homology search is a popular method that assists to predict biological roles by inference. However, it is very time consuming process as the rapid growing of sequence libraries. Use of sequence motifs and signature patterns is a convenient and speedy method to predict directly the biological functions. A new method to extract sequence motifs from groups of related proteins has been studied and the methodology was applied to analyze unknown protein sequences. The method was implemented as a computer tool on a UNIX workstation.

Another important theme of bioinformatics is the problem of databases. Recently, many bacteria genomes have been completely sequenced. To store and to publish the results of sequencing projects, database systems are indispensable. Since the purpose of genome sequencing is to understand biological functions from genetic information, the genome sequence database must also oriented to the biological function. As a model case of such database, Bacillus subtilis open reading frames database is constructed in collaboration with Prof. N. Ogasawara (NAIST) and Human Genome Center of the University of Tokyo. As the completion of sequencing of 1.3 Mbase regions by Japanese researchers groups, the first step of database construction has been finished and is released using WWW.

2. Cooperative Research Program for the Okazaki Large Spectrograph

The NIBB Cooperative Research Program for the Use of the OLS supports about 30 projects every year conducted by visiting scientists including foreign scientists as well as those in the Institute.

Action spectroscopical studies for various regulatory and damaging actions of light on living organisms, biological molecules, and organic molecules have been conducted (Watanabe, 1995, In CRC Handbook of Organic Photochemistry and Photobiology).

Publication List:
I. Faculty
Gualdi, R., Pascale, B., Zheng, M., Hamada, Y., Coleman J.R. and Zaret, K.S. (1996). Hepatic specification of the gut endoderm in vitro: cell signalling and transcriptional control. Gene Dev. 10, 1670-1682.
Hayashi, H., Mochii, M., Kodama, R., Hamada, Y., Mizuno, N., Eguchi, E. and Tachi, C. (1996). Isolation of a novel chick homolog of serrate and its coexpression with C-Notch1 in chick development. Int. J. Dev. Biol. 40, 1089-1096.
Higuchi, H., Kiyama, H., Hayakawa, T., Hamada, Y and Tsujimoto, Y.(1995). Differential Expression of Notch1 and Notch2 in developing and adult mouse brain. Mol. Brain Res. 29, 263-272.
Kato, H., Sakai, T., Tamura, K., Minoguchi, S., Shirayoshi, Y., Hamada, Y., Tsujimoto, Y. and Honjo, T. (1996). Functional conservation of mouse Notch receptor family members. FEBS lett. 395, 221-224.
Kawai, H., Nakamura, S., Mimuro, M., Furuya, M., Watanabe, M. (1996). Microspectrofluorometry of the autofluorescent flagellum in phototactic brown algal zoids. Protoprasma 191, 172-177.
Ogiwara, A., Ogasawara, N., Watanabe, M. and Takagi, T. (1996) Construction of the Bacillus subtilis ORF database (BSORF DB). Proc. Genome Informatics 1996, 228-229.
Ogiwara, A., Uchiyama, I., Takagi, T. and Kanehisa, M. (1996) Construction and analysis of a profile library characterizing groups of structurally known proteins. Protein Science, 5, 1991-1999.
Shinomura, T., Nagatani, A., Hanzawa, H., Kubota, M., Watanabe, M., Furuya, M. (1996). Action spectra for phytochrome A- and B-specific photoinduction of seed germination in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 93, 8129-8133.
Yamazaki. Y., Kataoka, H., Miyazaki, A., Watanabe, M., Ootaki, T. (1996) Action spectra for photoinhibition of sexual development in Phycomyces blakesleeanus. Photochem. Photobiol. 64, 387-395.
II. Cooperative Research Program for the Okazaki Large Spectrograph
Andrady, A. L., Torikai, A. and Kobatake, T. (1996). Spectral sensitivity of chitosan photodegradation. J. Appl. Polym. Sci. 62, 1465-1471.
Kawai, H., Nakamura, S., Mimuro, M., Furuya, M. and Watanabe, M. (1996). Microspectrofluorometry of the autoflulrescent flagellum in phototactic brown algal zoids. Protoplasma 191, 172-177.
Munakata, N., Morohashi, F., Hieda, K., Suzuki, K., Furusawa, Y., Shimura H. and Ito, T. (1996). Experimental correspondence between spore dosimetry and spectral photometry of solar ultraviolet radiation. Photochem. Photobiol. 63, 74-78.
Nakagawa, T., Umemura, S., Kakiuchi Y. and Ueda, T. (1996). Action spectrum for sporulation and photoavoidance in the plasmodium of Physarum polycephalum, as modified differentially by temperature and starvation. Photochem. Photobiol. 64, 859-862.
Saitow, F. and Nakaoka, Y. (1996). Photodynamic action of methylene blue on the Paramecium membrane. Photochem. Photobiol. 63, 868-873.
Shibata, H., Noda, T., Ogura, T., Suginaka, K., Matui, Y., Ozoe, Y., Sawa, Y. and Kono, Y. (1996). A soluble-form pf pro-oxidant lumazine from cyanobacterial cells generates superoxide anion under near-UV irradiation. Biochim. Biophys. Acta 1274, 129-134
Shichijo C., Hamada, T., Johnson, C. B. and Hashimoto, T. (1996). Effects of moderately low temperature on phytochrome responses during preirradiation: anthocyanin synthesis in Sorghum bicolor at high-end low-Pfr/Ptot ratios. Photochem. Photobiol. 63, 328-335.
Shinomura, T., Nagatani, A., Hanzawa, H., Kubota M., Watanabe, M. and Furuya, M. (1996). Action spectra for phytochrome A- and B-specific photoinduction of seed germination in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 93, 8129-8133.
Takeuchi Y., Murakami, M., Nakajima, N., Kondo, N. and Nikaido, O. (1996). Induction and repair of damage to DNA in cucumber cotyledons irradiated with UV-B. Plant Cell Physiol. 37, 181-187.
Tazawa, E., Fujiwara, A., Ishida, O. and Yasumasu, I. (1996). Photoactivation of NADH cytochrome c reductase in mitochondria islated form sperm, eggs and viscera of sea urchin, oyster, abalone and echiuroid. Comp. Biochem. Physiol. 114B, 245-250.
Yamazaki, Y., Kataoka, H., Miyazaki, M., Watanabe, M. and Ootaki, T. (1996). Action spectra for photoinhibition of sexual development in Phycomyces blakesleeanus. Photochem. Photobiol. 64, 387-392.
Yasumasu, I., Tazawa, E., Asami, K. and Fujiwara, A. (1996). Does the low respiratory rate in unfertilized eggs result mainly from depression of the redox reaction catalyzed by flavoproteins? Analysis of the respiratory system by light-induced release of CO-mediated inhibiton. Develop. Growth Differ. 38, 359-371.
Last Modified: 12:00, June 27, 1997