Proceedings of the Japan Academy, Series B
Online ISSN : 1349-2896
Print ISSN : 0386-2208
ISSN-L : 0386-2208
Volume 81 , Issue 9
Showing 1-5 articles out of 5 articles from the selected issue
Review
  • Hiroshi SUGA
    2005 Volume 81 Issue 9 Pages 349-362
    Published: 2005
    Released: January 20, 2006
    JOURNALS FREE ACCESS
    Of prime interest in numerous studies on water, an important substance to all living systems, may be its physical, chemical, biological characteristics in our internal and external environments. One of the central problems underlying all these researches is a basic structural problem. An important question was why ordinary ice did not obey the third law of thermodynamics. The proton-disordered phase Ih remains down to the lowest temperature without exhibiting any indication of phase transition. We found that the glass transition is not a characteristic property of liquid but of wide occurrence in condensed systems that failed to maintain thermal equilibrium during continuous cooling. Crystalline substance that exhibited freezing-in process on cooling was designated as "glassy crystals". In fact, ice Ih exhibited a glass transition at around 110 K due to slowing down of reorientational motion of the water molecules. A particular kind of impurity was found to accelerate dramatically the motion, and to induce a long-awaited phase transition at 72 K. The transition removed a substantial fraction of the residual entropy of ice. The dopant acted as a kind of catalysis for releasing the immobilized non-equilibrium state to recover thermal equilibrium in the laboratory time. Structure and some properties of the ordered low temperature phase, designated as ice XI, are discussed. The same ordering processes observed in some clathrate hydrates possessing hydrogen-bonded networks similar to ice Ih are described. Interplay between phase transformation and glass transition in relation to important role played by particular dopant is discussed.


    (Communicated by Syûzô SEKI, M.J.A.)
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  • Kiyoshi HORIKAWA, Masahiko ISOBE
    2005 Volume 81 Issue 9 Pages 363-381
    Published: 2005
    Released: January 20, 2006
    JOURNALS FREE ACCESS
    The study of coastal sediment processes was carried out initially by coastal geomorphologists in the past century. However, the dynamics of nearshore sediment movement has been treated by researchers in the fields of coastal engineering and nearshore oceanography over the past half century. The aim of this paper is to review the achievement of the related researches up to the present and to suggest finally the subjects which should be studied more deeply in the near future. This review article covers 1) the significance of coastal sediment study as an introduction, 2) an outline of coastal sediment behavior, 3) the critical water depth for the inception of sediment movement, 4) various modes of coastal sediment movement, 5) numerical simulation models of beach transformation, and 6) conclusions and recommendations for future studies.


    (Communicated by Takao INUI, M.J.A.)
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  • Nobuko OHMIDO, Kiichi FUKUI, Toshiro KINOSHITA
    2005 Volume 81 Issue 9 Pages 382-392
    Published: 2005
    Released: January 20, 2006
    JOURNALS FREE ACCESS
    Rice chromosome research was initiated around 1910 and has been progressing ever since. Twelve pairs of chromosomes (2n = 24) and a 440 Mb genome, the smallest genome among all main cereal crops, have been identified. According to the recent rice chromosome researches, all chromosomes were well identified over the disadvantages of small chromosome size and quantitative rice chromosomal maps have been developed using chromosome image analysis system (CHIAS). Moreover, agriculturally important genes have been detected using new direct DNA visualization methods with fluorescence in situ hybridization (FISH). This review describes the recent progress in molecular and digital cytogenetics using visualization from a historical perspective, highlighting the future prospects in rice chromosome science.


    (Communicated by Eishiro SHIKATA, M.J.A.)
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  • Eiko OHTSUKA, [in Japanese]
    2005 Volume 81 Issue 9 Pages 393-402
    Published: 2005
    Released: January 20, 2006
    JOURNALS FREE ACCESS
    Non-Watson-Crick-type hydrogen bonds involving minor nucleosides such as inosine in anticodon loops of transfer RNA are found in nucleic acids. Inosine contains hypoxanthine as a nucleobase and can form base pairs with various bases in the genetic decoding process. This property was applied to cloning complementary DNA by using oligodeoxyribonucleotide primers which contain deoxyinosine residues. Hypoxanthine is generated by deamination of adenine, one of the major nucleobases in DNA and RNA. Formation of unusual hydrogen bonds derived from damaged nucleobases in nucleic acids is thought to be main cause of disorders in genetic information flow. Mutagenesis and carcinogenesis of damaged bases, including hypoxanthine, 7, 8-dihydro-8-oxoguanine (8-oxoguanine) and pyrimidine photo-dimers in c-Ha-ras genes, were investigated by using synthetic genes containing modified nucleotides. The mode of recognition of unusual base pairing between a thymine photo-dimer and adenine by a repair enzyme was studied by X-ray analysis.



    (Communicated by Takashi SUGIMURA, M.J.A.)
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Original Paper
  • Masashi SUZUKI
    2005 Volume 81 Issue 9 Pages 403-409
    Published: 2005
    Released: January 20, 2006
    JOURNALS FREE ACCESS
    The DNA-binding specificity of archaeal transcription factors, FL10 (pot0377090, LrpA) and Ss/Sa-Lrp, was studied by re-analyzing foot-printing experiments carried out by other groups: Brinkman, A. B., et al., (2000) J. Biol. Chem. 275, 38160-38169, Enoru-Eta, J. et al., (2002) Mol. Microbiol. 45, 1541-1555, and Enoru-Eta, J. et al. (2000) J. Bacteriol. 182, 3661-3672. The two proteins are closely related, classified into the same group of FFRPs, feast/famine regulatory proteins. Many FFRPs, by forming dimers, bind DNAs in the 5-3-5 arrangement: N ANBNCND NE[TTT/AAA]NENDNCNBNA, where, e.g. NA is the base complementary to NA. In the light of this new observation, the ideal binding site of FL10 was identified as TTCGA[TCT/AGA]TCGAA or GTCGA[TCT/AGA]TCGAC. The ideal site recognized by Ss/Sa-Lrp was identified as ATTTT[TTT/AAA] AAAAT. By comparing these analyses with our experiments using another archaeal FFRP, FL11 (pot0434017), characteristics of the foot-prints shared by FFRPs were discussed.


    (Communicated by Masanori OTSUKA, M.J.A.)
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