  NATIONAL INSITUTE FOR BASIC BIOLOGY

National Institute for Basic Biology

RESEARCH SUPPORT FACILITY

Head of Facility:
Yoshinori Ohsumi (April 1, 1998-)

Associate Professor:
Masakatsu Watanabe

Research Associates:
Yoshio Hamada, (Tissue and Cell Culture)
Atsushi Ogiwara (Computer)

Post Doctral Fellow:
Mineo Iseki ¹ (Large Spectrograph ) (-October 31, 1998)

Technical Staffs:
Mamoru Kubota (Large Spectrograph)
Chieko Nanba (Plant Culture, Farm, Plant Cell)
Toshiki Ohkawa (Computer)
Kaoru Sawada (Tissue and Cell Culture)
Tomoki Miwa (Computer)
Sho-ichi Higashi (May 1, 1998-) (Large Spectrograph)
Makiko Ito (Large Spectrograph)
Misayo Masuda (Computer)
Keiko Suzuki (Plant Culture, Farm, Plant Cell)

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 30kW Xenon arc lamp and has a compound grating composed of 36 smaller individual gratings. It projects a spectrum of a wavelength range from 250nm (ultraviolet) to 1,000nm (infrared) onto its focal curve of 10m 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 tropical 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, 20W output), two CW dye lasers (Coherent, CR599-01) (420-930nm, 250-1000mW output), A/O modulators (up to 40MHz) to chop the laser beam, a beam expander, and a tracking microbeam irradiator (up to 200mm s^-1 in tracking speed, down to 2mm 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, many kind of computers are equipped: UNIX servers and engineering workstations (Sun Ultra Enterprise server, SPARC stations, IRIS machines, NEWS machines, etc.), and some personal computers (Macintosh¹s and Windows machines). All of these machines, as well as almost every PC in each laboratory, are connected each other with local area networks, which are also linked to the high performance multimedia backbone network of Okazaki National Research Institutes.

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, database retrievals, homology search services, and so on. Providing network communication services is also an important task of this laboratory. We maintain the World-Wide Web server that contains the NIBB home pages (URL is http://www.nibb.ac.jp).

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 under extraordinary environments such as strong light intensity, low or high temperatures.

5. Experimental Farm

This laboratory consists of two 20 m² glass-houses with precise temperature and humidity control, three green houses (each 6 m²) at the P1 physical containment level, a small farm, two greenhouses (45 and 88 m²) with automatic sprinklers, two open aquariums (30 and 50t) 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 cleanbenches, 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 (30km 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 transduction 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 (Matsunaga et al., 1998). Photo-receptive and signal transduction 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: Today, many kinds of genome structures of various organisms have been revealed. Using these genomic sequence data, we performed a comprehensive sequence analysis especially for Bacillus subtilis. Microbial genomics has entered a new era of functional analysis, and bioinformatics is also shifting to support the functional analysis. We have developed a knowledge base system for the transporter system of B. subtilis. The system not only represents functional information but also helps to discriminate transporter genes in newly determined genomic sequences.

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

Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M. (1998). DBGET/LinkDB: an Integrated Database Retrieval System. Pacific Symposium on Biocomputing '98, 683-694.

Atsushi Ogiwara (1998). Systematic Classification of B. subtilis Genes and Construction of a Knowledge Base to Represent Functional Information. Proc. Genome Informatics 1998, 310-311.

Furukawa, T., Watanabe, M. and Shihira-Ishikawa, I. (1998). Green- and Blue-Light-mediated chloroplast migration in the centric diatom, Pleurosira laevis. Protoplasma. 203, 214-220.

Matsunaga, S., Hori, T., Takahashi, T., Kubota, M., Watanabe, M., Okamoto, K., Masuda, K. and Sugai, M. (1998). Discovery of signaling effect of UV-B/C light in the extended blue~UV-A-type action spectra for step-down and step-up photophobic responses in the unicellular flagellate alga Euglena gracilis. Protoplasma 201, 45-52.

Mimuro, M., Tamai, N., Murakami, A., Watanabe, M., Erata, M., Watanabe, M.M., Tokutomi, M. and Yamazaki, I. (1998) Multiple pathways of the excitation energy flow in the phtosynthetic pigment system of a cryptophyta, Cryptomonas sp. (CR-1). Phycological Res., 46, 155-164.

II. Cooperative Research Program for the Okazaki Large Spectrograph

Furukawa, T., Watanabe, M. and Shihira-Ishikawa, I. (1998). Green- and Blue-Light-mediated chloroplast migration in the centric diatom, Pleurosira laevis. Protoplasma. 203, 214-220.

Furusawa, Y., Quintern, L.E., Holtschmidt, H., Koepke, P. and Saito, M. (1998). Determination of erythema-effective solar radiation in Japan and Germany with a spore monolayer film optimized for the detection of UVB and UVA -results of a field campaign. Appl. Microbiol Biotechnol. 50, 597-603.

Munakata, N., Ono, M. and Watanabe, S. (1998). Monitoring of solar-UV exposure among schoolchildren in five japanese cities using spore dosimeter and UV-coloring Labels. Jpn. J. Cancer Res. 89, 235-245.

Shinomura, T., Hanzawa, H., Schäfer, E. and Furuya, M. (1998). Mode of phytochrome B action in the photoregulation of seed germination in Arabidopsis thaliana. Plant J. 13, 583-590.

Takeuchi, Y., Murakami, M., Nakajima, N., Kondo, N. and Nikaido, O. (1998). The photorepair and photoisomerization of DNA lesions in etiolated cucumber cotyledons after irradiation by UV-B depends on wavelength. Plant Cell Physiol. 39, 745-750.

Torikai, A. and Hasegawa, H. (1998). Wavelength effect on the accelerated photodegradation of polymethylmethacrylate. Polym. Degradn. Stab. 61, 361-364.

Torikai, A., Kobatake, T. and Okisaki, F. (1998). Photodegradation of polystyrene containing flame retardants. J. Appl. Polym. Sci. 67, 1293-1300.

Torikai, A. (1998) Wavelength sneistivity in the photodegradation of polymethylmehtacrylate: Accelerated degradation and gel formation. In "Science and Technology of Polymers and Advanced Materials". (Prasad, P. N. et al. ed.), Plenum Press, New York, pp. 581-586.

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Last Modified: 12:00, May 28, 1999