RESEARCH SUPPORT FACILITY

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 spectro-scopical 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 200 µm s^-1 in tracking speed, down to 2 µm 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

Computer laboratory maintains several computers to provide computation resources and means of electronic communication in this Institute. Currently, the main system consists of three servers and two terminal work-stations: biological information analysis server (SGI Origin 2000), database server (Sun Enterprise 450), file server (Sun Enterprise 3000), data visualization terminal and molecular simulation terminal (both are SGI Octanes). Some personal computers and color/monochrome printers are also equipped. On this system, we provide various biological databases and data retrieval/analysis programs, and support large-scale data analysis and database construction for the Institute members.

Computer laboratory also provides network communi-cation services in the Institute. Most of PCs in each laboratory as well as all of the above service machines are connected each other with local area network (LAN), which is linked to the high performance multimedia backbone network of Okazaki National Research Institute (ORION). Many local services including sequence analysis service, file sharing service and printer service are provided through this LAN. We also maintain a public World Wide Web server that contains the NIBB home pages (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. The laboratory also includes a building with storage and work space.

6. Plant Cell Laboratory

Autotrophic and heterotrophic culture devices and equipment for experimental cultures of plant and microbial cells in this laboratory. 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 found 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 National Institute for basic Biology). The laboratory provides a variety of growth chambers that precisely control the conditions of plant growth and dacilities for molecular biological and physiological enaluations of transgenic plants.

The laboratory is also a base of domestic and international collaborations devorted 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 unicellular 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. Photo-receptive and signal transduction mecha-nisms of algal gene expression were also studied by action spectroscopy.

(2) Developmental Biology: Replacement of the ankyrin repeats of mouse Notch2 gene with E.coli b-gactosidase gene induces early embryonic lethality around E10.5. The lethality was suggested due to defects in extraembryonic tissues, because the mutant embryo grew and differentiated further in vitro. Histological exami-nation and in situ hybridization analysis with trophoblast subtype-specific probes revealed that the development of giant and spongiotrophoblast cell layers are normal in the mutant placenta, while vasculogenesis in the labyrinth layer apperaed compromised at E9.5. Since the lethality was circumvented by production of chimeric mice with tetraploidy wild type embryos, we concluded that the embryonic lethality is due to defect in growth and/or differentiation of labyrinthine trophoblast cells. The mutant embryo, however, could not be rescued in the tetraploid chimeras beyond E12.5 because of insurfficient development of umbilical cord, indicating another role of Notch2 signaling in the mouse development. Chimeric analysis with diploid wild type, however, revealed contribution of mutant cells to these affected tissues by E13.5. Thus, Notch2 are not cell autonomously required for the early cell fate determination of labyrinthine trophoblast cells and allantoic mesodermal cells, but plays an indispensable role in the further formation of functional labyrinth layer and umbilical cord.

(3) Computational Biology: Comparative genomics is a useful approach to find clues to understanding complex and diverse biological systems from rapidly growing genome database. We have constructed a database system for comparative analysis of many of microbial genomes ever sequenced and are developing new compu-tational techniques for large-scale genome sequence comparison. Especially, we are developing a method for orthologous grouping among multiple genomes, which is a crucial step for comparative genomics. In addition to splitting fusion genes into orthologous domains, we are also enhancing the grouping algorithm to incorporate the information of gene arrangement on the genome.

In parallel, we have developed a tool to incorporate various sequence features such as G+C contents, codon usage bias and locations of repetitive elements into the genome comparison. By this approach, we made detailed comparison of closely related microbial genomes to investigate the genomic polymorphisms or evolutionary changes in collaboration with Dr. I. Kobayashi's group (Univ. Tokyo), including comparative genome analysis of two strains of Staphylococcus aureus.

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 scien-tists 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". pp, 1276 - 1288).

Publication List:

I. Faculty

Kondou, Y., Nakazawa, M., Higashi, S., Watanabe, M. and Manabe, K. (2001) Equal-quantum action spectra indicate fluence-rate-selective action of multiple photoreceptors for photomovement of the thermophilic cyanobacterium Synechococcus elongatus. Photochem. Photobiol.73, 90-95.

Kumano, K., Chiba, S., Shimizu, K., Yamagata, T., Hosoya, N., Saito, T., Takahashi, T., Hamada, Y., Hirai, H. (2001) Notch1 inhibits differentiation of hematopoietic cells by sustaining GATA-2 expression. Blood98: 3238-9.

Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., Cui, L, Oguchi, A., Aoki, K., Nagai, Y., Lian, J., Ito, T., Kanamori, M., Matsumaru, H., Maruyama, A., Murakami, H., Hosoyama, A., Mizutani-Ui, Y., Takahashi, N.K., Sawano, T., Inoue, R., Kaito, C, Sekimizu, K., Hirakawa, H., Kuhara, S, Goto, S., Yabuzaki, J., Kanehisa, M., Yamashita, A., Oshima, K., Furuya, K., Yoshino, C., Shiba, T., Hattori, M., Ogasawara, N., Hayashi, H., Hiramatsu, K. (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus, The Lancet357, 1225-1240.

Lenci, F. and Watanabe, M. (2001) Photomovements and light sensing systems. In "Photobiology in the 21st Century" (eds. T. Coohil, D.-P. Häder, D. Valenceno) Valdemaer Press

Nakamura, S., Mikamori, M., Hiramatsu, M., Eura, S., and Watanabe, M. (2001) Specutacular fluorescence emission in sea urchin larvae. Zool. Sci. 18, 807-810.

Nakamura, S., Ogihara, H., Jinbo, K., Tateishi, M., Takahashi, T., Yoshimura, K., Kubota, M., Watanabe, M., and Nakamura, S. (2001) Chalamydomonas reinhardtii Dangeard (Chlamydomonadales, Chlorophyceae) mutant with multiple eyespots. Phycol. Res.49, 115-122.

Negishi, T., Nagaoka, C., Hayatsu, H., Suzuki, K., Hara, T., Kubota, M., Watanabe, M., and Hieda, K. (2001) Somatic-cell mutation induced by UVA and monochromatic UV radiation in repair-proficient and -deficient Drosophila melanogaster. Photochem. Photobiol.73, 493-498.

Watanabe, M. and Erata, M. (2001) Yellow-light sensing phototaxis in cryptomonad algae. In "Photomovement" (eds. D.-P. Häder and M. Lebert) pp. 343-373. Elsevier

II. Cooperative Research Program for the Okazaki Large Spectrograph

Hasegawa, E., Sawada, K., Akamatsu, T., Fujita, K. and Tamai, M. (2001) Fish behaviour control by the optical fiber optomotor reaction device. Bull. Nat. Res. Inst. Fish. Eng.22, 27-33.

Inada, C., Kudo, T., Yoshizumi, K., Takatori, K., Hedge, A. (2001) Effect of light irradiation wavelength on the inactivation of Penicillium. Bokin Bobai.12, 757-762.

Kakiuchi, Y., Takahashi,T., Murakami, A. and Ueda, T. (2001) Light irradiation induces fragmentation of the plasmodium, a novel photomorphogenesis in the true slime mold Physarum polycephalum: action spectra and evidence for involvement of the phytochrome. Photochem Photobiol.73, 324-329.

Kondou, Y., Nakazawa, M., Higashi, S., Watanabe, M. and Manabe, K. (2001) Equal-quantum action spectra indicate fluence-rate-selective action of multiple photoreceptors for photomovement of the thermophilic cyanobacterium Synechococcus elongatus. Photochem. Photobiol.73, 90-95.

Negishi, T., Nagaoka, C., Hayatsu, H., Suzuki, K.,Hara, T., Kubota, M., Watanabe, M. and Hieda, K. (2001) Somatic-cell mutation induced by UVA and monochromatic UV radiation in repair-proficient and deficient Drosophila melanogaster. Photochem. Photobiol.73, 493-498.

Yoshizumi, K., Kudo, T., Imaizumi, A., Fujinami, N.(2001) Action spectrum of light fastness of carthamin dyed on silk fabric under the irradiation of UV and visible light. SENI GAKKAISHI 57 No.9