Shin-ichiro Kajiyama

Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.

The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ∼95% of the gene-containing regions with the average G + C content was 34.3%. A total of 40 929 complete and partial structures of protein encoding genes have been deduced. Comparison with genes of other plant species indicated that 1529 (4%) of the putative protein-encoding genes are specific to the Euphorbiaceae family. A high degree of microsynteny was observed with the genome of castor bean and, to a lesser extent, with those of soybean and Arabidopsis thaliana. In parallel with genome sequencing, cDNAs derived from leaf and callus tissues were subjected to pyrosequencing, and a total of 21 225 unigene data have been generated. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with 12 J. curcas lines collected from various parts of the world to estimate their genetic diversity. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with J. curcas, especially in the fields of environment-related research such as biofuel production. Further information on the genomic sequences and DNA markers is available at http://www.kazusa.or.jp/jatropha/.

Analysis and experimental assessment of the sensitivity of stimulated Raman scattering microscopy

We theoretically show that the shot-noise-limited sensitivity of stimulated Raman scattering (SRS) microscopy, which enables high-contrast vibrational imaging, is similar to that of coherent anti-Stokes Raman scattering microscopy. We experimentally confirm that the sensitivity of our SRS microscope is lower than the shot-noise limit only by <15 dB, which indicates that the high-sensitivity of SRS microscopy is readily available.

Antimicrobial constituents of Angelica dahurica roots

One novel coumarin from Angelica dahurica roots was elucidated to be 5,8-di(2,3-dihydroxy-3-methylbutoxy)-psoralen. It occurs together with six other known coumarins and ferulic acid. The antimicrobial activity of the coumarins and ferulic acid were compared.

Stimulated Raman scattering microscope with shot noise limited sensitivity using subharmonically synchronized laser pulses

We propose and demonstrate the use of subharmonically synchronized laser pulses for low-noise lock-in detection in stimulated Raman scattering (SRS) microscopy. In the experiment, Yb-fiber laser pulses at a repetition rate of 38 MHz are successfully synchronized to Ti:sapphire laser pulses at a repetition rate of 76 MHz with a jitter of <8 fs by a two-photon detector and an intra-cavity electro-optic modulator. By using these pulses, high-frequency lock-in detection of SRS signal is accomplished without high-speed optical modulation. The noise level of the lock-in signal is found to be higher than the shot noise limit only by 1.6 dB. We also demonstrate high-contrast, 3D imaging of unlabeled living cells.

DNA aptamers that bind to chitin

We have succeeded in the acquisition of DNA aptamers that recognize chitin using in vitro selection. The obtained DNA aptamers have the stem-loop or bulge loop structures with guanine rich loop clusters and the clockwise B-form stems.

Nostofungicidine, an antifungal lipopeptide from the field-grown terrestrial blue-green alga Nostoc commune

Abstract In the course of our screening program for bioactive compounds, a novel lipopeptide, nostofungicidine ( 1 ), was isolated from the methanolic extract of a fiel-grown terrestrial blue-green alga, Nostoc commune . The structure of nostofungicidine was elucidated by chemical degradation and extensive NMR measurements including DQF-COSY, HOHAHA, HMBC, and ROESY techniques. Nostofungicidine contains a novel β-amino acid, 3-amino-6-hydroxy stearic acid (Ahs) in its structure.

Trichosetin,a Novel Tetramic Acid Antibiotic Produced in Dual Culture of Trichoderma harzianum and Catharanthus roseus Callus

The dual culture of Trichoderma harzianum and Catharanthus roseus callus produced an antimicrobial compound with a remarkable activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus subtilis. Structural elucidation revealed that this compound, which we have named trichosetin, is a novel tetramic acid (2,4-pyrrolidinedione) antibiotic and a homolog of the fungal metabolite equisetin. This compound however, was not produced in the individual culture of T. harzianum or C. roseus callus.

Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin

Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-Cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin.

Phytotoxicity of the tetramic acid metabolite trichosetin

Trichosetin, a tetramic acid-containing metabolite produced in the dual culture of Trichoderma harzianum and Catharanthus roseus (L.) G. Don callus, was subjected to phytotoxicity assays. In seedling growth assays, trichosetin inhibited root and shoot growth of all five plant species tested by damaging the cell membrane, as evidenced by the dose-dependent increase in electrolyte leakage and lipid peroxidation. Vital staining of trichosetin-treated Nicotiana tabacum BY-2 cells, with rhodamine 123, showed a weaker green fluorescence compared to controls indicating damaging effects on mitochondria. FDA-PI staining, to determine cell viability, indicated that cells of the trichosetin-treated roots were mostly dead.

Paenibacillus glycanilyticus sp. nov., a novel species that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune

A novel bacterial strain, DS-1T, was isolated that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune. The isolate was identified by a combination of phenotypic characterization, cellular fatty acid analysis, DNA base composition, DNA-DNA hybridization and 165 rRNA gene sequence analysis. Phylogenetic analysis placed strain DS-1T within the Paenibacillus cluster on a phylogenetic tree and the phenotypic characteristics of this strain appear to be similar to those of Paenibacillus curdlanolyticus IFO 15724T and Paenibacillus kobensis IFO 15729T. The strain was distinguished from P. curdlanolyticus IFO 15724T and P. kobensis IFO 15729T by its ability to degrade the polysaccharide of Nostoc commune, by assimilation of rhamnose, inositol and L-fucose and by its wide range of optimal growth temperature (28-37 degrees C). Like other Paenibacillus species, this strain contains anteiso-C15:0 as a major cellular fatty acid, and it has a DNA G+C content of 50.5 mol %. Based on these results, it is concluded that this isolate should be placed within a novel species of Paenibacillus, Paenibacillus glycanilyticus sp. nov., with the type strain DS-1T (= IFO 16618T = JCM 11221T = NRRL B-23455T).