Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats 1 . Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published 2,3 , analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination 4-6 and developmental genetics 7 . In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including 2,900 new genes, using 59-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.We applied the whole-genome shotgun approach to an inbred strain, , derived from the southern Japanese population, as the main target. A total of 13.8 million reads amounting to approximately 10.6-fold genome coverage were obtained from the shotgun plasmid, fosmid and bacterial artificial chromosome (BAC) libraries. A newly developed RAMEN assembler was used to process the shotgun reads to generate contigs and scaffolds. The N50 values (50% of nucleotides in an assembly are in scaffolds-or contigs-longer than or equal to the N50 value) are ,1.41 megabases (Mb) for scaffolds and ,9.8 kilobases (Kb) for contigs. The total length of the contigs reached 700.4 Mb, which, from now on, we refer to as the medaka genome size.To construct ultracontigs, the scaffolds were integrated with the medaka genetic map by using SNP markers. For this purpose, we further obtained about 2.8-fold coverage of shotgun reads from another inbred strain HNI (refs 9, 10), which is derived from the northern Japanese population. The reads were assembled by RAMEN to scaffolds covering 648 Mb. Aligning the HNI contigs with the HdrR genome using BLASTZ 11 , we identified 16.4 million SNPs as well as 1.40 million insertions and 1.45 million deletions in non-repetitive regions (Supplementary Table 2). We selected 2,401 SNPs and genetically mapped them onto medaka chromosomes using a backcross panel between the...

The synthesis of corilagin was achieved by the integration of the development of the oxidative coupling of the symmetrically protected gallates and the temporarily ring-opened synthetic route for the 3,6-hexahydroxydiphenoyl (HHDP) bridge. This is the first total synthesis of the 1C4/B-ellagitannins, which contain ring-flipped glucose.

Identification of the mRNA start site is essential in establishing the full-length cDNA sequence of a gene and analyzing its promoter region, which regulates gene expression. Here we describe the development of a 5'-end serial analysis of gene expression (5' SAGE) that can be used to globally identify transcriptional start sites and the frequency of individual mRNAs. Of the 25,684 5' SAGE tags in the HEK293 human cell library, 19,893 matched to the human genome. Among 15,448 tags in one locus of the genome, 85.8%-96.1% of the 5' SAGE tags were assigned within -500 to +200 nt of mRNA start sites using the RefSeq, UniGene and DBTSS databases. This technique should facilitate 5'-end transcriptome analysis in a variety of cells and tissues.

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This paper describes a total synthesis of (-)-strictinin, an ellagitannin that is 1-O-galloyl-4,6-O-(S)-hexahydroxydiphenoyl (HHDP)-β-D-glucose. In the study, total efficiency of the synthesis was improved to produce a 78% overall yield in 13 steps from D-glucose. In the synthesis, formation of the 4,6-(S)-HHDP bridge including the 11-membered bislactone ring was a key step, in which intramolecular aryl-aryl coupling was adopted. The coupling was oxidatively induced by CuCl2-n-BuNH2 with perfect control of the axial chirality, and the reaction conditions of this coupling were optimized thoroughly to achieve the quantitative formation of the bridge.

An RNA oligomer, r(GGACGAGUCC), which mimics the metal ion-binding motif of hammerhead ribozymes, was shown to fold by itself into a conformation possessing a metal ion binding property which is similar to that of the intact ribozyme (Tanaka, et al. J. Am. Chem. Soc. 2000, 122, 11303-11310). To determine the metal ion-binding site of this motif at an atomic level, we synthesized a series of RNA oligomers which were selectively labeled with a (15)N-labeled guanosine at each of the four guanosine residues. The (15)N-chemical shift perturbation with Cd(II) ions by one-dimensional (1D) (15)N NMR spectra showed that the chemical shift of the N7 of the G7 residue, N7/G7, in the metal ion-binding motif was specifically perturbed. This is the first experimental evidence to prove that the N7/G7 binds with a Cd(II) ion.

Amphotericin B (AmB) is thought to exert its pharmacological effects by forming a barrel-stave assembly with ergosterol in fungal membranes. To examine the interaction between AmB and ergosterol (Erg) or cholesterol (Cho), (13)C- and (19)F-labelled covalent conjugates were prepared as reported previously (N. Matsumori et al. Chem. Biol. 2004, 11, 673-679). The CD spectra of the conjugates in a membrane-bound form suggested that the distance between the heptaene moieties of the ergosterol conjugates AmB-C(2)-(6-F)Erg 2 and AmB-C(2)-Erg 3 is similar to that of AmB in ergosterol-containing membranes, but significantly larger than that of AmB in nonsterol or cholesterol-containing membranes. These observations suggest that, as is the case with ergosterol-containing membranes, the conjugated sterol moiety prevents the close contact between the heptaene moieties within the membrane that would reduce channel conductivity of the AmB assemblies. To further investigate this bimolecular interaction, we recorded the solid-state NMR spectra of conjugates 2 and AmB-C(2)-(6-F)Cho 4, which are composed of uniformly (13)C-labelled AmB and 6-fluorinated ergosterol or cholesterol; the conjugates were expected to facilitate the estimation of distances between the fluorine and carbon atoms. By using rotor-synchronous double resonance (rotational echo double resonance of X cluster; RDX) experiments, we deduced the distance between the fluorine atom and its nearest carbon atom in the heptaene moiety of 2 to be less than 8.6 A. This indicates that the B ring of ergosterol comes close to the AmB polyene moiety. A conformational search of the AmB-ergosterol conjugate by using distance constraints derived from the RDX results suggested that ergosterol molecules possibly surround the AmB assembly, which is in contrast with the conventional image in which ergosterol is inserted into AmB molecules.

To compare the crystalline-state conformations of MαNP acid esters with those existing in the solution state, X-ray crystallographic analyses of 22 MαNP esters and two MαNP acids were carried out. It was found that all 27 conformers observed in the solid state have structures in which the 2-CH 3 group and the 2Ј-H of the naphthyl group are synperiplanar and are almost always located in the same plane. In addition, the CH 3 -O7-C2-C1 moiety in all cases has an antiperiplanar structure within the MαNP plane. From further analyses, 22 conformers adopt the so-called syn structure, in which the O7-C2-C1-O6 moiety is synperiplanar. On the other hand, the remaining five conformers have the so-called anti structure. With regard to the rotational conformation around C1ЈЈ-O5, all conformers have structures similar to the synperiplanar conformation. In the so-called syn conformers, the interatomic distance d(H8Ј-O6) is distributed between 2.48 Å and 2.96 Å, while the distance d(H8Ј-O7) varies between 2.26 Å and 2.56 Å, indicating the weak bifurcated hydrogen