Highly efficient isothermal DNA amplification system using three elements of 5'-DNA-RNA-3' chimeric primers, RNaseH and strand-displacing DNA polymerase

We developed an efficient method of isothermally amplifying DNA termed ICAN, Isothermal and Chimeric primer-initiated Amplification of Nucleic acids. This method allows the amplification of target DNA under isothermal conditions at around 55 degrees C using only a pair of 5'-DNA-RNA-3' chimeric primers, a thermostable RNaseH and a DNA polymerase with strong strand-displacing activity. ICAN is capable of amplifying DNA at least several times greater than the amount produced with PCR by increasing primer concentration. This method would be applicable for on-site DNA detection including gene diagnosis, and would also be suitable for 'real time' detection when combined with a cycling probe.     

Degradation of wood and enzyme production by Ceriporiopsis subvermispora

The degradation of the components of Japanese beech and Japanese cedar wood was measured over time in cultures of the white-rot fungus Ceriporiopsis subvermispora. Although there was no initial degradation of cedar wood, after 12 weeks the mass loss of both cedar and beech wood was 15–20%. The mass losses of filter paper in beech wood-containing cultures and glucose cultures after 12 weeks were 87% and 70%, respectively. The ratio of lignin loss to mass loss of both beech and cedar wood cultures approached 2.0. Although the cellulose loss in cedar wood was very low throughout the 12-week incubation, C. subvermispora degraded the hemicellulose in Japanese cedar much more effectively than that in Japanese beech. These results confirm that C. subvermispora is a selective lignin degrader. During the 12-week incubation with Japanese beech wood, C. subvermispora continuously produced at least one of three phenol oxidases: laccase was produced initially, followed by Mn-independent peroxidase activity peaking at 6 weeks and Mn-dependent peroxidase activity peaking at 10 weeks. Lignin peroxidase and carboxymethylcellulase activities peaked after 3 weeks of incubation. Avicelase activity was present throughout the incubation period, although the activity was very low. The low-molecular-mass fraction of the extracellular medium, which catalyzes a redox reaction between O₂ and electron donors to produce hydroxyl radical, may act synergistically with the enzymes to degrade wood cell walls.     

Gizzard myoglobin contents and feeding habits in avian species

In an attempt to consider physiological function of myoglobin (Mb), we determined Mb contents of gizzard smooth muscles with special reference to feeding habits in 85 avian species of 19 orders. The Mb content in 44 species of herbivorous birds was 7.52+/-3.81 mg/g wet muscle, which was significantly higher than the value of 2.34+/-1.74 mg/g in 41 species of carnivorous ones (P<0.001). Buffering capacity, as determined by in vitro titration method, was 37.3+/-5.5 slykes/g in gizzard smooth muscles of 75 species and 60.7+/-10.5 slykes in breast skeletal muscles of 77 species (P<0.001), which suggests a significantly higher dependence, almost comparable to cardiac muscles, of the gizzard muscular function on aerobic metabolism. Together with the fact that blood circulation in the gizzard is very low at resting, and might be further limited during activity, we conclude that the higher Mb content in gizzards of herbivorous birds is an adaptation, to allow storage and/or facilitated diffusion of oxygen, during process of high mechanical work required to grind down hard and fibrous vegetable food under the conditions of limited circulatory supply.     

The equilibrium unfolding intermediate observed at pH 4 and its relationship with the kinetic folding intermediates in green fluorescent protein

Folding mechanisms of a variant of green fluorescent protein (F99S/M153T/V163A) were investigated by a wide variety of spectroscopic techniques. Equilibrium measurements on acid-induced denaturation of the protein monitored by chromophore and tryptophan fluorescence and small-angle X-ray scattering revealed that this protein accumulates at least two equilibrium intermediates, a native-like intermediate and an unfolding intermediate, the latter of which exhibits the characteristics of the molten globule state under moderately denaturing conditions at pH 4. To elucidate the role of the equilibrium unfolding intermediate in folding, a series of kinetic refolding experiments with various combinations of initial and final pH values, including pH 7.5 (the native condition), pH 4.0 (the moderately denaturing condition where the unfolding intermediate is accumulated), and pH 2.0 (the acid-denaturing condition) were carried out by monitoring chromophore and tryptophan fluorescence. Kinetic on-pathway intermediates were accumulated during the folding on the refolding reaction from pH 2.0 to 7.5. However, the signal change corresponding to the conversion from the acid-denatured to the kinetic intermediate states was significantly reduced on the refolding reaction from pH 4.0 to pH 7.5, whereas only the signal change corresponding to the above conversion was observed on the refolding reaction from pH 2.0 to pH 4.0. These results indicate that the equilibrium unfolding intermediate is composed of an ensemble of the folding intermediate species accumulated during the folding reaction, and thus support a hierarchical model of protein folding.     

Increased resistance of mercury-coupled hemoglobins to alkali.

Yeast cells derepress their biosynthetic enzymes for arginine, histidine, lysine and tryptophan upon starvation for any one of these amino acids. This concerted derepression appears to be a manifestation of a general control over amino acid biosynthesis. Two classes of mutation that destroy this control are described in detail. Both classes are recessive to the wild-type allele. One class, aas, is unable to derepress the enzymes of arginine, histidine, lysine or tryptophan biosynthesis. The other class, tra, is fully derepressed for the enzymes of all these pathways of amino acid biosynthesis. This latter class is temperature-sensitive for growth. Analysis of the temperature-sensitive lesion indicates that tra3 mutants, when grown at 36 °C, are defective in the cell cycle early in the G1 phase. Strains carrying the tra3 mutation arrest as single, unbudded cells at the non-permissive temperature regardless of their position in the cell cycle at the time of the shift to the restrictive temperature. The position of the tra3 step in the cell cycle has been determined with respect to other cell-cycle events, and has been found to act at the same point in the cycle as the α factor-sensitive step. The dual role of the TRA3 gene product in general regulation and in cell division suggests that information on the state of amino acid biosynthesis is part of the signal for “start” in the cell cycle.     

Transposon tagging in rice

To develop an efficient gene isolation method for rice we introduced the maize Ac/Ds system into rice. Extensive analysis of their behavior in rice for several generations indicated that Ac and Ds in the presence of Ac transposase gene actively transpose in rice. A wide spectrum of mutations affecting growth, morphogenesis, flowering time and disease resistance have been obtained in the population carrying Ac/Ds and some of them were genetically analyzed. Main efforts are currently being made to isolate genes responsible these mutations. In addition, a number of Ac/Ds were mapped on chromosomes and mapped elements will be used in the future for directed tagging of genes with known chromosomal positions.     

A novel method for determination of α1,6fucosyltransferase activity using a reducing oligosaccharide from egg yolk as a specific acceptor

A new method for determination of 1,6fucosyltransferase activity has been described. Recently, the disialyl-biantennary undecasaccharide was prepared in high yield from egg yolk [(1996), Carbohydr Lett 2: 137–42]. By treatment of this oligosaccharide with neuraminidase and -galactosidase, we readily obtained an asialo-agalacto-biantennary heptasaccharide (GlcNAc 1,2Man1,6[GlcNAc1,2Man1,3]Man1,4GlcNAc1,4GlcNAc). Using this asialo-agalacto-oligosaccharide as an acceptor, fucosyltransferases from human plasma and extracts of various human hepatoma cell lines were assayed in the presence of GDP-[3H]fucose. The reaction mixture was applied to a column of GlcNAc-binding, Psathyrella velutina lectin coupled gel. All the fucosylated acceptor were bound to the column which was eluted with 50 mM GlcNAc. Structural analyses revealed that only the innermost GlcNAc residue of the acceptor was fucosylated through an 1,6-linkage, and the oligosaccharide prepared could be used as a specific acceptor for 1,6fucosyltransferase. The present method was used to screen plasma 1,6fucosyltransferase in several patient groups, and significantly elevated activities were found in samples from patients with liver diseases, including chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma.     

Initial nitrogen content and topographic moisture effects on the decomposition of pine needles

The effects of litter quality and site characteristics on the decomposition process were investigated using a litterbag method. Pine needle litters with differing nitrogen concentrations (0.8, 0.6 and 0.4%) were placed on the upper and lower slopes of a Pinus thunbergii Parl. plantation. After both 3 and 6 months, the mass of decomposing litter with the lower nitrogen concentration was larger than the litter with higher nitrogen concentrations. After 9 months, there were no significant differences in the litter mass remaining, regardless of the initial nitrogen concentration. Moisture content in the litter was always higher on the lower slope, although the mass of litter was smaller. Nitrogen concentration of the decomposing litter increased linearly with accumulated mass loss. The increase in nitrogen concentration of decomposing litter was greater on the lower slope, but this increase did not differ between initial nitrogen concentrations. The nitrogen release from the decomposing litter with higher initial nitrogen concentration was larger than the release from litter bags with lower nitrogen concentrations. This result suggests that there may be positive feedback between soil nutrient availability, litter quality and nutrient release from decomposing litter at the intraspecific level.     

Formation of acyl radical in lipid peroxidation of linoleic acid by manganese-dependent peroxidase from Ceriporiopsis subvermispora and Bjerkandera adusta.

Lipid peroxidation by managanese peroxidase (MnP) is reported to decompose recalcitrant polycyclic aromatic hydrocabon (PAH) and nonphenolic lignin models. To elucidate the oxidative process, linoleic acid and 13(S)-hydroperoxy-9Z,11E-octadecadienoic acid [13(S)-HPODE] were reacted with MnPs from Ceriporiopsis subvermispora and Bjerkandera adusta and the free radicals produced were analyzed by ESR. When the MnPs were reacted with 13(S)-HPODE in the presence of Mn(II), H2O2 and tert-nitrosobutane (t-NB), the ESR spectrum contained a sharp triplet of acyl radical (aN = 0.81 mT). Formation of acyl radical was also observed in the reactions of Mn(III)-tartrate with 13(S)-HPODE and with linoleic acid, but the latter reaction occurred explosively after an induction period of around 30 min. Reactions of MnP with linoleic acid in the presence of Mn(II), H2O2 and t-NB gave no spin adducts while addition of t-NB after preincubation of linoleic acid with MnP/Mn(II)/H2O2 for 2 h gave spin adducts of carbon-centered (aN = 1.53 mT, aH = 0.21 mT) and acyl (aN = 0.81 mT) radicals. In contrast to linoleic acid, methyl linoleate and oleic acid were not peroxidized by MnP and chelated Mn(III) within a few hours, indicating that structures containing both the 1,4-pentadienyl moiety and a free carboxyl group are necessary for inducing the peroxidation in a short reaction time. These results indicate that MnP-dependent lipid peroxidation is not initiated by direct abstraction of hydrogen from the bis-allylic position during turnover but proceeds by a Mn(III)-dependent hydrogen abstraction from enols and subsequent propagation reactions involving the formation of acyl radical from lipid hydroperoxide. This finding expands the role of chelated Mn(III) from a phenol oxidant to a strong generator of free radicals from lipids and lipid hydroperoxides in lignin biodegradation.