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 .

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.

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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.

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 tetramerformsacentralporewithdimensionsof23Å indiameterand ϳ50 Å in depth. -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.Vibrio parahaemolyticus is a Gram-negative marine bacterium known to be one of the major causes of pandemic seafoodborne gastroenteritis. V. parahaemolyticus possesses two circular replicons of 3.2 and 1.9 megabase pairs, which might confer an advantage by enabling DNA replication in seawater of lower temperature and/or low nutritional value (1, 2). Such an advantage would potentially increase risks of food intoxication by allowing explosive expansion of the population of the microorganism. Hemolysis on Wagatsuma agar (a blood agar), known as the Kanagawa phenomenon, is associated with human pathogenic strains of V. parahaemolyticus. A major virulence factor of this pathogen is the thermostable direct hemolysin (TDH) 7 (3-5), which has a variety of biological activities including hemolytic activity, cardiotoxicity, and enterotoxicity. There are two copies of the tdh gene (or its homologue trh) in pathogenic V. parahaemolyticus, indicating the importance of this exotoxin for survival of the organism (2). The mature form of TDH consists of 165 amino acids, including a single intramolecular disulfide bond, but no close homologue of TDH has been found in other organisms. The significance of Arg 46 , Gly 62 , Trp 65 , and Gly 90 residues on hemolysis was determined by site-directed mutagenesis (3, 6).The common features of the bacterial pore-forming toxin are as follows. 1) It is released as a soluble monomer into the extra-bacterial space. 2) It oligomerizes to form a pore at the host cell membrane (7,8). An earlier study reported that TDH acted as a pore-forming toxin, creating a functional pore ϳ20 Å in diameter (reviewed in Ref. 3). We previously constructed a low resolution C 4 symmetric model of tetrameric TDH in solution based on small angle x-ray scattering (SAXS), transmission electron microscopy (TEM), and analytical ultracentrifugation (9). However, the precise structure and the mechanism for its pore-forming toxicity are still unknown. Several bacterial toxins, including TDH, show paradoxical responses to heat treatment, known as the Arrhenius effect (10, * This study was s...

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.

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The P450 cytochrome monooxygenase gene, ltxB, was cloned and overexpressed in Escherichia coli as a 6xHis-tagged protein. The resulting recombinant LtxB was purified by Ni-NTA affinity chromatography and characterized biochemically. Purified LtxB demonstrated typical cytochrome P450 spectroscopic properties including substrate-induced transition from a low-spin (lambdamax=414 nm) to high-spin state (lambdamax=386 nm) upon incubation with N-methyl-L-valyl-L-tryptophanol. The catalytic activity of LtxB was verified by demonstrating the oxidation/cyclization of N-methyl-L-valyl-L-tryptophanol to (-)-indolactam V. LtxB shows a relaxed specificity for analogue substrates in which the valyl group is substituted for other aliphatic groups. The relaxed substrate specificity of LtxB, along with the relaxed specificity of the prenyltransferase, LtxC, allowed for the enzymatic production of a series of (-)-indolactam V and lyngbyatoxin analogues.