RESEARCH SUPPORT FACILITY


                              NATIONAL INSTITUTE FOR BASIC BIOLOGY

RESEARCH SUPPORT FACILITY

Head of Facility:: Yoshiaki Suzuki
Associate Professor:: Masakatsu Watanabe
Research Associates:: Yoshio Hamada (Tissue and Cell Culture)
Kenta Nakai (Computer)
Technical Staff:: Mamoru Kubota
Chieko Nanba
Toshiki Ohkawa
Kaoru Sawada
Tomoki Miwa
Mariko Saitoh (-May 30)
Kimiko Yamamiya
Takeshi Mizutani
Sonoko Ohsawa (Aug. 4-)

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 is dedicated to cooperative use under the NIBB Cooperative Research Program for the Use of the Okazaki Large Spectrograph.

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 (ultra-violet) 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 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, 20 W output), two CW dye lasers (Coherent, CR-599-01) (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 um s-1 in tracking speed, down to 2 um 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 levels. 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 (VAX11/780 and micro VAX II), UNIX workstations (SPARC stations IPC, IPX, and 10; DEC station 2100), and personal computers (PC9801, IBM compatible machines, and Macintosh). Through Ethernet or CDDI, all of them are linked to the backbone FDDI of our institute, which is further linked to the new hyper multimedia network of Okazaki National Research Institutes (the ORION network). Each laboratory has at least two computers connected to the network and all sites linked to the Internet are accessible from there. In addition, NetWare server machines (Quarter L and DECpc) works as file servers and printer servers. Latest databases and softwares of various kinds are also maintained.

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 20 m2 glass-houses with precision temperature and humidity control, a limited farm, two greenhouses (45 m2, 88 m2) with automatic sprinklers and window control two open aquariums (30 t, 50 t) 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 experimenatal cultures of plant and microbial cells.

7. Molecular Biological Analysis Laboratory

In order to facilitate molecular biological analyses, high performance equipments such as DNA sequencers (ABI 370A; 373A-18), peptide synthesizers (ABI 430A and 431A), a nucleotide synthesizer (ABI 381A), imaging analyzers (Fuji BAS 2000-3060 and 3080; tein analysis system (Takara Glyco-Tag) are provided.

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 by measuring computerized-videomicro-scopically the motile behavior of the cells at the cellular and subcellular levels. 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. Currently, there are two projects. One is to develop an expert system to predict various protein localization sites from amino acid sequence data. The other is to construct a prediction system of mature mRNA sequence from their precursors. The former work is done in cooperation with Dr. A. Goffeau (Univ. Catholique Louvain, Belgium) et al. of yeast genome sequencing group and Dr. T. Shimizu (Hirosaki Univ.). Currently, we are trying to find a reliable way to predict transmembrane segments of membrane proteins correctly. The latter work is a cooperatiori with Dr. H. Sakamoto (Kobe Univ.) and we are now focusing on the study of aberrant and alternative splicing events: we have constructed a novel databese containing aberrant splicing mutations of mammalian genes (Nakai and Sakamoto, Gene, 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.

Publication List:

I. Faculty

Goffeau, A., Slonimski, P., Nakai, K., and Risler, J. L. (1993) How many yeast genes encode for membrane spanning proteins? Yeast 9, 691-702.

Goffeau, A., Nakai, K., Slonimski, P., and Risler, J. L. (1993) The membrane proteins encoded by yeast chromosome III genes. FEBS Lett. 325, 112-117.

Goto, N., Yamamoto, K. T. and Watanabe, M. (1993) Action spectra for inhibition of hypocotyl growth of wild-type plants and of the hy2 Ionghypocotyl mutant of Arabidopsis thaliana L. Photochem. Photobiol. 57, 867-871.

Kataoka, H. and Watanabe, M. (1993) Negative phototropism in Vaucheria terrestris regulated by calcium III. The role of calcium characterized by use of a high-power argon-ion laser as the source of unilateral blue light. Plant Cell Physiol. 34, 737-744.

Saitou, T., Tachikawa, Y., Kamada, H., Watanabe, M. and Harada, H. (1993) Action spectrum for light-induced formation of adventitious shoots in hairy roots of horseradish. Planta 189, 590-592.

Takahashi, T. and Watanabe, M. (1993) Photosynthesis modulates the sign of phototaxis of wild-type Chlamydomonas reinhardtii. Effects of red background illumination and 3-(3',4'- dichlorophenyl)- 1,1-dimethylurea. FEBS Lett. 336, 516-520.

II. Cooperative Research Program for the Okazaki Large Spectrograph

Matsunaga, T., Hatakeyama, Y., Ohta, M., Mori, T. and Nikaido, O. (1993) Establishment and characterization of a monoclonai antibody recognizing the Dewar isomers of (6-4)photoproducts. Photochem. Photobiol. 57, 934-940.

Mitsuoka, T., Torikai, A. and Fueki, K. (1993) Wavelength sensitvity of the photodegradation of poly(methyl methacrylate). J. Appl. Polym. Sci. 47, 1027-1032.

Oishi, T. and Ohashi, K. (1993) Effects of wavelengths of light on the photoperiodic gonadal response of blindedpinealectomized Japanese quail. Zool. Sci. 10, 757-762.

Okazaki, N., Mori, Y. and Hanazaki, I. (1993) Effect of adding starch on the photo-inhibition of oscillation in the "Briggs-Rauscher" reaction. Chem. Lett. 1135-1138.

Saitou, T., Tachikawa, Y., Kamada, H., Watanabe, M. and Harada, H. (1993) Action spectrum for light-induced formation of adventitious shoots in hairy roots of horseradish. Planta 189, 590-592.

Sasaki, M., Takeshita, S., Sugiura, M., Sudo, N., Miyake, Y., Furusawa, Y., and Sakata, T. (1993) Ground-based observation of biologically active solar ultraviolet-B irradiance at 35 N latitude in Japan. J Geomag. Geoelectr. 45, 473-485.

Sekiguchi, T., Mori, Y. and Hanazaki, I. (1993) Photo-response of the [Ru(bpy)3]2+/Br03-/H+ system in a continuous-flow stirred tank reactor. Chem. Lett. 1309-1312.

Shichijo, C., Hamada, T., Hiraoka, M., Johnson, C. B. and Hashimoto, T. (1993) Enhancement of red light-induced anthocyanin synthesis in sorghum first internodes by moderate low temperature given in the preirradiation culture period. Planta 191, 238-245.

Tada, M. (1993) Methods for investigating photoregulated carotenogenesis. In Methods in Enzymology 214 (L. Packer ed.). Academic Press, San Diego, pp.269-267.

Takahashi, T. and Watanabe, M. (1993) Photosynthesis modulates the sign of phototaxis of wild-type Chlamydomonas reinhardtii. Effects of red background illumination and 3-(3',4'-dichlorophenyl)-1,1-dimethylurea. FEBS Lett. 336, 516-520.

Torikai, A., Kato, H., Fueki, K., Suzuki, Y., Okisaki, F., and Nagata, M. (1993) Photodegradation of polymer materials containing flame-cut agents. J. Appl. Polym. Sci. 50, 2185-2190.

Torikai, A., Mitsuoka, T. and Fueki, K. ( 1993) Wavelength sensitivity of the photoinduced reaction in polycabonate. J. Polym. Sci. 31, 2785-2788.