Similarity graphing and enzyme-reaction database: methods to detect sequence regions of importance for recognition of chemical structures

We developed a new method which searches sequence segments responsible for the recognition of a given chemical structure. These segments are detected as those locally conserved among a sequence to be analyzed (target sequence) and a set of sequences (reference sequences). Reference sequences are the sequences of functionally related proteins, ligands of which contain a common chemical substructure in their molecular structures. 'Similarity graphing' cuts target sequences into segments, aligns them with reference sequence pairwise, calculates the degree of similarity for each alignment, and shows graphically cumulative similarity values on target sequence. Any locally conserved regions, short or long in length and weak or strong in similarity, are detected at their optimal conditions by adjusting three parameters. The 'enzyme-reaction database' contains chemical structures and their related enzymes. When a chemical substructure is input into the database, sequences of the enzymes related to the input substructure are systematically searched from the NBRF sequence database and output as reference sequences. Examples of analysis using similarity graphing in combination with the enzyme-reaction database showed a great potentiality in the systematic analysis of the relationships between sequences and molecular recognitions for protein engineering.     

Somatic embryogenesis and plant regeneration from the anther of Aconitum carmichaeli Debx

Anthers of Aconitum carmichaeli Debx. were used for callus induction. After the addition of 5 ppm 2,4-D and 1 ppm kinetin callus induction occurred over a period of 15 weeks. When calluses were subcultured on a medium containing 1 ppm 2,4-D for 12 weeks embryogenesis occurred. Mature somatic embryos developed normal shoots when transferred to basal medium inoculated with 1 ppm GA and 5 ppm BAP. Rooting occurred after the transfer of shoots to a new medium containing 0.5 ppm IAA and plantlets formed. The transplantation of these was successful and all plants matured during 5 months subsequent cultivation.     

Two novel diterpenes from bark of Cinnamomum cassia

Two new diterpenes were isolated from the fraction exhibiting anti-allergic activity obtained from the bark of Cinnamomum cassia. They have been given the trivial names cinncassiol D₄ and cinncassiol D₄ glucoside and their structures determined on the basis of chemical and spectral evidence.     

Bitter phenylpropanoid glycosides from Conandron ramoidioides

A new bitter glycoside, conandroside and a known glycoside, acteoside were isolated from Conandron ramoidioides. On the basis of the chemical and spectral evidence, conandroside was shown to be 2-(3′,4′-dihydroxy-phenyl)-ethanol 1-O-β-D-xylosyl-(1 → 3)-β-D-(4-caffeyl)-glucoside.     

Porphyromonas gingivalis induces the production of interleukin‐31 by human mast cells,resulting in dysfunction of the gingival epithelial barrier

Interleukin (IL)‐31 is important for innate immunity in mucosal tissues and skin, and increased IL‐31 expression participates in the pathogenesis of chronic inflammatory diseases affecting the skin, airways, lungs, and intestines. We investigated the contribution of mast cells to the induction of IL‐31 production following infection with the periodontal pathogen, Porphyromonas gingivalis. We found that oral infection with P. gingivalis increased IL‐31 expression in the gingival tissues of wild‐type mice but not in those of mast cell‐deficient mice. The P. gingivalis‐induced IL‐31 production by human mast cells occurred through the activation of the JNK and NF‐κB signalling pathways and was dependent on the P. gingivalis lysine‐specific protease gingipain‐K. P. gingivalis infection induced IL‐31 receptor α and oncostatin M receptor β expression in human gingival epithelial cells. Notably, the P. gingivalis‐induced IL‐31 production by mast cells led to the downregulation of claudin‐1, a tight junction molecule, in gingival epithelial cells, resulting in an IL‐31‐dependent increase in the paracellular permeability of the gingival epithelial barrier. These findings suggest that IL‐31 produced by mast cells in response to P. gingivalis infection causes gingival epithelial barrier dysfunction, which may contribute to the chronic inflammation observed in periodontitis.     

Specific translocation of tuftsin (Thr-Lys-Pro-Arg), a natural immunomodulating peptide, into the nuclei of human monocytes

To delineate the mechanism of growth and differentiation activities of tuftsin (Thr-Lys-Pro-Arg), we examined the translocation of tuftsin after internalization by the target cells. We found using two independent techniques, fluorescence microscopy and autoradiography, that while in human polymorphonuclear leukocytes (terminally differentiated cells) the peptide remains in the cytoplasmic compartment, in monocytes it translocates to the nucleus. The ability of tuftsin to directly interact with DNA was documented by a large increase in the melting point of bovine DNA in the presence of tuftsin. It is suggested that the translocation, processing and action of tuftsin may depend on the differentiation state and/or on the type of effector cells. Also, tuftsin has the capacity to interact directly with DNA and, therefore, may have a potential for affecting gene activity.     

Alterations in the protein synthetic apparatus of Friend erythroleukemia cells infected with vesicular stomatitis virus or herpes simplex virus.

We have compared the effects of infection with herpes simplex virus (HSV) and vesicular stomatitis virus (VSV) on the protein synthetic apparatus of Friend erythroleukemia cells. Previous studies demonstrated that infection with HSV rapidly shuts off the synthesis of globin and other cellular polypeptides (Y. Nischioka and S. Silverstein, 1977, Proc. Natl. Acad. Sci. U.S.A. 74: 2370-2374). In contrast to these findings, globin synthesis persists in Friend erythroleukemia cells infected with VSV. Physical measurements of the size of bulk-infected cell mRNA, using hybridization with polyuridylic acid, demonstrated that there was no detectable change in the size of mRNA's after infection with VSV. A comparison of the kinetics of hybridization of cytoplasmic RNA extracted from cells infected with either HSV or VSV with globin complementary DNA revealed that by 4 h postinfection with HSV only about 15% of the globin mRNA sequences remained, whereas there was no discernible change in the sequence abundance of globin mRNA in VSV-infected cells.     

Role of polyamines in cytokinesis of mammalian cells

Inhibition of polyamine biosynthesis in mammalian cells with methylglyoxal bis-(guanylhydrazone) and α-methyl ornithine inhibits cytokinesis and induces the formation of binucleate cells. Further, these binucleate cells exhibited a diffused pattern of microfilaments compared with the control cells as evidenced by indirect immunofluorescence using anti-actin antibodies. These effects can be reversed by increasing the intracellular levels of the polyamines. The results of this study suggest that polyamines may have a role in the process of cytokinesis and cell division.     

The relationship between levels and rates of synthesis of polyamines during mammalian cell cycle

The objective of this study was to examine the rate of synthesis and the intracellular levels of polyamines as a function of the HeLa cell cycle. The intracellular levels of ornithine, which were high during mitosis and early G1 phase, decreased rapidly during late G1 phase when the ornithine decarboxylase activity was at its peak. The activities of ornithine decarboxylase and S-adenosyl methionine decarboxylase reached a peak during G1 and decreased rapidly during the S phase. The levels of polyamines were maximum in mitosis and S phase. In constrast, the rate of polyamine synthesis during S phase was 5–10 fold lower than that in mitosis or G1 phase. We have also observed fluctuations in diamine-oxidase activity during the cell cycle. The enzyme activity was high during mitosis and late G1 and low during S phase. Thus, the results of this study suggest an important role for the catabolic enzymes in the regulation of polyamine levels during the mammalian cell cycle.