The Facility provides large- and medium-scale equipments 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.
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 gratingsurface 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 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 safety 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 needes in this Institute, various computers are equipped: VAX/VMS machines, UNlX workstations (SPARCstation 10 and others), and personal computers of various vendors. Through the Ethernet or the CDDI, all of them are linked to the backbone FDDI of this institute, which is further linked to the hyper-multimedia network of Okazaki National Research Institutes (the ORION network). Each laboratory has several computers connected to the network and full resources of the Internet are accessible from there. In addition, NetWare server machines work as file servers and printer servers. Latest databases and various useful softwares are also maintained. Information of this institute, including this document is open to the world through the World Wide Web (WWW; URL is http://www.nibb.ac.jp).
4. Plant Culture Laboratory
There are a large number of culture boxes, cubicles, and a limited number of rooms with environmental control for plant culture.
5. Experimental Farm
This laboratory consists of two 20m2 glass-houses with precision temperature and humidity control, a limited farm, two greenhouses (45m2, 88m2) with automatic sprinklers and window control two open aquariums (30t, 50t) and several smaller tanks. The laboratory also includes a building with office, storage and work-space.
6. Plant Cell Culture Laboratory
Autotrophic and heterotrophic culture devices and equipped for experimental cultures of plant and microbial cells.
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 growih chambers that precisely control the conditions of plant growth and facilities for molecular biological, biochemical, 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, in press) by measuring computerized-videomiceographs of the motile behavior of the cells at the cellular and subcellular levels (Erata et al. (1995) Protoplasma , in press). Photoreceptive and signal tranduction mechanisms of algal gametogenesis are also studied by action spectroscopy.
(2) Developmental Biology: Myosin is a ubiquitous protein in eukaryotes. It is presumed that this molecule plays a key role in cell motility as well as other functions. The role of myosis in non-muscle cells might be better understood if wildtype cell could be compared with mutant cells with altered myosin molecules, though such mutants have not been isolated. The faculty intends to examine the function of the myosin heavy chain in vertebrate non-muscle cells by interrupting its synthesis with the introduction of antisense RNA molecules.
(3) Computational Biology: Efforts to develop new methodology for sequence analysis have been continued. One of the projects is to develop an expert system to predict various protein localization-sites from amino acid sequence data. This work is done in collaboration with Drs. S. Miyano (Kyushu Univ.), T. Shimizu (Hirosaki Univ.) and A. Bairoch (Geneva Univ.). Some results have been Published in Shimizu and ZK. Nakai (Proc. Genome Informatics Workshop 1994, 148-149) and in K. Nakai, A. Shinohara, and S. Miyano (Proc. GIW 1994, 170-171). Another is to construct a prediction system of mature mRNA sequence from their precursors. It is in collaboration with Drs. H. Sakamoto (Kobe Univ.), Y. Akiyama (Kyoto Univ.) and S. Stamm (Cold Spring Harbor Lab.). The activities of computer assistance for other experimental researchers can be exemplified in M. Tomita, J. Kobayashi, AA. Mori, K. Hagiwara, K. Nakai, Y. Suzuki, and S. Miyajima, Protein Eng., 7, in press.
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, in press).
Publication List:
I. Faculty
Nakai, K. and Sakamoto, H. (1994) Construction of a novel database containing aberrant splicing mutations of mammalian genes, Gene,141, 171-177.
Nakai, K., Tokimori, T., Ogiwara, A., Uchiyama, I., and Niiyama, T. (1994) Gnome - an Internet-based sequence analysis tool, Comp. Appl. Biosci ., 10, 547-550.
II. Cooperative Research Program for the Okazaki Large Spectrograph
Andrady, A.L., Amin, M.B., Hamid, S.H., Hu, X. and Torikai, A. (1994) Effects of increased solar ultraviolet radiation on materials. In Environmental Effects of Ozone Depletion: 1994 Assessment (J.C. van der Leun, X. Tang and M. Tevini, eds.), United Nations Environment Programme (UNEP), Nairobi. pp. 101-110.
Hashimoto, T. (1994) Requirements of blue, UV-A, and UV-B light for normal growth of higher plants, as assessed by action spectra for growth and related phenomena. In Proceedings of International Lighting in Controlled Environments Workshop (T.W. Tibbitts, ed.), NASA Ames Research Center, Moffett Field, CA., USA, pp. 143-157.
Hashimoto, T. (1994) UV-B effects on plant: The present knowledge and prospect for future studies. In Proceedings of the Tsukuba Ozone Workshop-Grobal Environment Tsukuba '94, (K. Takemoto and S. Nishioka, eds.), Center for Grobal Environmental Research, Japan, pp. 134-145.
Nikaido, O., Ohta, M. and Matsunaga, T. (1994) Detection of the Dewar photoproducts in solar light-exposed DNA by a damage specific monoclonal antibody and the repair of the photoproducts in human cells. In The 13th UOEH International Symposium & The 2nd Pan Pacific Cooperative Symposium on Inpact of Increased UV-Exposure on Human Health and Ecosystem (Y. Kodama and Si Duk Lee, eds.), University of Occupational and Environmental Health, pp. 190-193.
Sasaki, M., Takeshita, S., Sugiura, M. and Sakata, T. (1994) An increase in the global solar ultraviolet-B irradiance at 35oN in Japan since 1990. J. Geomag. Geoelectr.46, 827-834.
Todo, T., Ryo, H., Takemori, H., Toh, H., Nomura, T. and Kondo, S. (1994) High-level expression of the photorepair gene in Drosophila ovary and its evolutionary implications. Mutation Research, DNA Repair315, 213-228
National Insitute for Basic Biology
