Ecological aspects of the Japanese eel, Anguilla japonica, collected from coastal areas of Japan

The ecological characteristics of 597 yellow and silver-stage Japanese eels, Anguilla japonica, were examined and compared among collection sites located at three different latitudes of Japan (Amakusa Islands, Mikawa Bay, and Sanriku Coast) to provide basic data on this unusual catadromous fish species. Eels were sexed and their total length, body weight, age, and growth rate based on otolith analysis was compared among sexes, stages, and collection sites. The overall sex ratio favored females (94%), but the sex ratio differed among the three locations. The frequency of females was highest in the coastal waters at Sanriku in the north (100%), next highest at Mikawa Bay in central Japan (95%), and lowest in the Amakusa Islands in the south (70%). Silver eel males ranged from 41.2-66.3 cm in length and 4-10 years in age, and silver eel females from 44.3-97.2 cm in length and 5-17 years in age. Female eels generally grew faster (8.7+/-2.2 cm/year) than males (6.4+/-2.6 cm/year), and the growth rate slowed in the older eels. The growth rate of A. japonica at all three sites was much faster than that of other temperate anguillid species (< 4 cm/year), and their age at maturation was younger than that of other temperate species (approximately 7 to > 50 years), suggesting this species has important ecological differences from other similar species.     

Immunoassay using microfluid filters constructed by deep X-ray lithography

Microfluid filters were fabricated, which possessed 2,100 cylindrical through-bores (psi 40 microm) in 200 microm-thickness polymethylmethacrylate (PMMA) sheets (psi 3 mm), by deep X-ray lithography using synchrotron radiation. To evaluate the microfluid filters as a device for an immunoassay, we bound the goat anti-mouse immunoglobulin G (IgG) antibody to the surface of the filters, and set the filters between reaction vessels stacked vertically in a microreactor. An enzyme-linked immunosorbent assay (ELISA) of mouse IgG using the goat anti-mouse IgG/horseradish-peroxidase (HRP) conjugate indicated that mouse IgG could be quantitatively detected in the range of 0-100 ng/ml, demonstrating the applicability of vertical microfluidic operation to the immunoassay.     

Isolation of the antioxidant pyranonigrin-A from rice mold starters used in the manufacturing process of fermented foods

Rice mold starters prepared from Aspergillus species are commonly used for the manufacture of koji in the production of oriental fermented foods. Methanol extracts of rice mold starters fermented by the Aspergillus species, A. awamori, A. kawachii, A. oryzae, A. saitoi, and A. sojae, were examined for their antioxidative activity by using a 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging system. The extracts of A. awamori, A. kawachii, and A. saitoi exhibited higher activity than those of A. oryzae and A. sojae. An antioxidant was isolated from the extract of A. saitoi and identified as pyranonigrin-A by 1H-NMR, 13C-NMR, and FAB-MS analyses. The antioxidative activity of pyranonigrin-A was approximately equivalent to that of ferulic acid, an antioxidant in cereal grain. It was present in rice mold starters prepared by A. awamori, A. kawachii, and A. saitoi, although there was no pyranonigrin-A in the A. oryzae and A. sojae starters. The results suggest that the content of pyranonigrin-A in rice mold starters has a correlation with the antioxidative activity, and that it is induced in rice mold starters at the sporulation stage.     

Identification of 6-substituted 4-arylsulfonyl-1,4-diazepane-2,5-diones as a novel scaffold for human chymase inhibitors

A novel series of 6-substituted 4-sulfonyl-1,4-diazepane-2,5-diones were designed, synthesized and evaluated as human chymase inhibitors. Structure-activity relationship studies led to the identification of a potent inhibitor, (6S)-6-(5-chloro-2-methoxybenzyl)-4-[(4-chlorophenyl)sulfonyl]-1,4-diazepane-2,5-dione, with an IC(50) of 0.027 microM.     

Heterogeneous environment of the S-H group of Cys966 near the flavin chromophore in the LOV2 domain of Adiantum neochrome1

The primary photochemistry of the blue-light sensor protein, phototropin, is adduct formation between the C4a atom of the flavin mononucleotide (FMN) chromophore and a nearby, reactive cysteine (Cys966), following decay of the triplet excited state of FMN. The distance between the C4a position of FMN and the sulfur atom of Cys966 is 4.2 A in the LOV2 domain of Adiantum neochrome 1 (neo1-LOV2), a fusion protein of phototropin containing the phytochrome chromophoric domain. We previously reported the presence of an unreactive fraction in neo1-LOV2 at low temperatures, which presumably originated from the heterogeneous environment of Cys966 [Iwata, T., Nozaki, D., Tokutomi, S., Kagawa, T., Wada, M., and Kandori, H. (2003) Biochemistry 42, 8183-8191]. The present study showed that (i) 28% forms an adduct at 77 K (state I), (ii) 50% forms an adduct at 150 K but not at 77 K (state II), and (iii) 22% does not form an adduct at 150 K (state III). By Fourier transform infrared (FTIR) spectroscopy, we observed the S-H stretching frequencies at 2570 and 2562 cm-1 for state I and at 2563 cm-1 for state II, suggesting that the microenvironment of the S-H group of Cys966 determines the reactivity at low temperatures. Adduct formation is more efficient for state I than for states II and III. Molecular dynamics simulation strongly suggests that the observed multiple structures originate from the isomeric forms of Cys966. We thus concluded that there are multiple local structures of FMN and cysteine in neo1-LOV2, each of which is thermally converted by protein fluctuation at physiological temperatures.     

Development of O-acyl isopeptide method

During over a decade of study on aspartic protease inhibitors and water-soluble prodrugs, in 2003, we discovered that the presence of an O-acyl instead of N-acyl residue within the peptide backbone significantly changed the secondary structure of the native peptide. In addition, the target peptide was subsequently generated by an O-N intramolecular acyl migration reaction. These findings led to the development of a novel method, called "O-acyl isopeptide method," for the synthesis of peptides containing difficult sequence. Further application of the method to Alzheimer's Abeta1-42 revealed that the O-acyl isopeptide of Abeta1-42 could be effectively synthesized and stored without spontaneous self-assembly. Intact monomer Abeta1-42 could then be obtained from the isopeptide under physiological experimental conditions. We named the O-acyl isopeptide as "Click Peptide," because of its "quick and easy one-way conversion" to the parent Abeta1- 42. Application of the click peptide has provided a new basis for the investigation of the biological functions of Abeta1-42 by inducible activation of its self-assembly. The O-acyl isopeptide method has further evolved as a general method for peptides synthesis with our recent developments of "O-acyl isodipeptide units" and "racemization-free segment condensation methodology." Isodipeptide units have enabled routine use of the O-acyl isopeptide method by avoiding the often difficult esterification reaction on resin. "Racemizationfree segment condensation methodology" has been achieved by employing N-segments possessing a C-terminal urethaneprotected O-acyl Ser/Thr residues. The synthesis of long peptides/proteins by racemization-free segment condensation has thus become possible at Ser/Thr residues instead of Cterminal Gly/Pro residues. As the O-acyl isopeptide method becomes more widely utilized, we have composed this review to facilitate its application for the production of peptides and proteins.     

The short arm of laminin gamma2 chain of laminin-5 (laminin-332) binds syndecan-1 and regulates cellular adhesion and migration by suppressing phosphorylation of integrin beta4 chain

The proteolytic processing of laminin-5 at the short arm of the gamma2 chain (gamma2sa) is known to convert this laminin from a cell adhesion type to a motility type. Here, we studied this mechanism by analyzing the functions of gamma2sa. In some immortalized or tumorigenic human cell lines, a recombinant gamma2sa, in either soluble or insoluble (coated) form, promoted the adhesion of these cells to the processed laminin-5 (Pr-LN5), and it suppressed their migration stimulated by serum or epidermal growth factor (EGF). Gamma2sa also suppressed EGF-induced tyrosine phosphorylation of integrin beta4 and resultant disruption of hemidesmosome-like structures in keratinocytes. Gamma2sa bound to syndecan-1, and this binding, as well as its cell adhesion activity, was blocked by heparin. By analyzing the activities of three different gamma2sa fragments, the active site of gamma2sa was localized to the NH(2)-terminal EGF-like sequence (domain V or LEa). Suppression of syndecan-1 expression by the RNA interference effectively blocked the activities of domain V capable of promoting cell adhesion and inhibiting the integrin beta4 phosphorylation. These results demonstrate that domain V of the gamma2 chain negatively regulates the integrin beta4 phosphorylation, probably through a syndecan-1-mediated signaling, leading to enhanced cell adhesion and suppressed cell motility.     

The urea transporter DUR3 contributes to rice production under nitrogen‐deficient and field conditions

Nitrogen is one of the most important elements for plant growth, and urea is one of the most frequently used nitrogen fertilizers worldwide. Besides the exogenously‐supplied urea to the soil, urea is endogenously synthesized during secondary nitrogen metabolism. Here, we investigated the contribution of a urea transporter, DUR3, to rice production using a reverse genetic approach combined with localization studies. Tos17 insertion lines for DUR3 showed a 50% yield reduction in hydroponic culture, and a 26.2% yield reduction in a paddy field, because of decreased grain filling. Because shoot biomass production and shoot total N was not reduced, insertion lines were disordered not only in nitrogen acquisition but also in nitrogen allocation. During seed development, DUR3 insertion lines accumulated nitrogen in leaves and could not sufficiently develop their panicles, although shoot and root dry weights were not significantly different from the wild‐type. The urea concentration in old leaf harvested from DUR3 insertion lines was lower than that in wild‐type. DUR3 promoter‐dependent β‐glucuronidase (GUS) activity was localized in vascular tissue and the midribs of old leaves. These results indicate that DUR3 contributes to nitrogen translocation and rice yield under nitrogen‐deficient and field conditions.     

Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions

The catalytic reaction of copper amine oxidase proceeds through a ping-pong mechanism comprising two half-reactions. In the initial half-reaction, the substrate amine reduces the Tyr-derived cofactor, topa quinone (TPQ), to an aminoresorcinol form (TPQ_amr) that is in equilibrium with a semiquinone radical (TPQ_sq) via an intramolecular electron transfer to the active-site copper. We have analyzed this reductive half-reaction in crystals of the copper amine oxidase from Arthrobacter globiformis. Anerobic soaking of the crystals with an amine substrate shifted the equilibrium toward TPQ_sq in an “on-copper” conformation, in which the 4-OH group ligated axially to the copper center, which was probably reduced to Cu(I). When the crystals were soaked with substrate in the presence of halide ions, which act as uncompetitive and noncompetitive inhibitors with respect to the amine substrate and dioxygen, respectively, the equilibrium in the crystals shifted toward the “off-copper” conformation of TPQ_amr. The halide ion was bound to the axial position of the copper center, thereby preventing TPQ_amr from adopting the on-copper conformation. Furthermore, transient kinetic analyses in the presence of viscogen (glycerol) revealed that only the rate constant in the step of TPQ_amr/TPQ_sq interconversion is markedly affected by the viscogen, which probably perturbs the conformational change. These findings unequivocally demonstrate that TPQ undergoes large conformational changes during the reductive half-reaction.