Biomedical subjects

Hiroaki Abe

Publications and source records attributed to Hiroaki Abe.

8 recordsLinked to original sources

PubMed2026

The complete sequence of the silkworm W chromosome uncovers its rapid evolution by large-scale duplications/deletions and translocation of W-linked genes.

The complete sequence of the W chromosome, which carries feminization activity in the silkworm, is crucial for understanding the sex-determination system in Lepidoptera. However, extensive accumulation of transposons due to lack of recombination, the very rare protein-coding genes and almost no information about molecular markers has hindered full W sequencing. We report the first complete silkworm W sequence (T2T_W, 11683305 bp) obtained by combining sequencing-assembly technologies and newly developed error detection methods, evaluated with genetically mapped W-RAPD markers, W-mutants, and W-derived BAC clones. The T2T_W sequence showed that the W is composed of a massive 92% accumulation of transposons and repeat sequences, among which the main constituents are intact LTR/LINE retrotransposons indicating recent expansions. In addition to Fem clusters producing Fem piRNA (Feminizer-derived PIWI-interacting RNA), we found 26 protein-coding genes in the W sequence. These include four gene pairs encoding zinc-finger motifs designated z1:z20 and a gene encoding serine/arginine repetitive matrix protein 1-like (SRRM1-like). To identify candidate genes for female sex-determination and differentiation we also sequenced the shortest W (3.8 Mb) from a translocation mutant with feminizing activity, which harbored four conventional genes: a Fem cluster, a pair of z1:z20 isoforms, z20-S, and a SRRM1-like gene. Phylogenetic analysis revealed that z1:z20 originated from a copy of an autosomal zinc-finger gene pair, z2:z21, translocated onto the W around 2.43 Mya and subsequently amplified to yield 4 W-linked zinc-finger gene pairs. The complete W sequence revealed that large-scale deletions and amplifications played a significant role in W chromosome evolution.

Animals↗

PubMed2006

Screening of C60 crystallization using a microfluidic system.

We have carried out screening of C60 crystallization using a simple liquid/liquid interfacial precipitation method in a microfluidic device. By controlling the time, temperature, and concentration, various metastable phases of C60 crystals were found, including tubes, spheres, open-ended hollow columns, stars, branches, and trees. The obtained C60 crystal shapes are similar to those of snow crystals. These findings suggest an urgent need to screen C60 crystallization for the development of fullerene C60 drugs.

Crystallization↗

PubMed2006

Bisabolane-type sesquiterpenes from the aerial parts of Lippia dulcis.

Six new bisabolane-type sesquiterpenes, peroxylippidulcines A-C (3-5), peroxyepilippidulcine B (6), and epilippidulcines B (7) and C (8), have been isolated from the aerial parts of Lippia dulcis, along with two known bisabolane-type sesquiterpenes, seven known flavonoids, and a known triterpenoid. The structures of 3-8 were characterized on the basis of NMR, MS, specific rotation, and X-ray crystallographic analysis data and chemical evidence.

Crystallography, X-Ray↗

PubMed2006

New iridoid glucosides from the aerial parts of Verbena brasiliensis.

Two new iridoid glucosides, verbenabraside A (1) and verbenabraside B (2), were isolated from the aerial parts of Verbena brasiliensis VELL., along with six known iridoid glucosides, gelsemiol 3-O-beta-D-glucoside (3), verbraside (4), 9-hydroxysemperoside (5), griselinoside (6), aralidioside (7), and 6alpha-hydroxyforsythide dimethyl ester (8), three known phenylethanoid glycosides, 2-phenylethyl O-beta-D-xylopyranosyl-(1-->2)-beta-D-glucopyranoside (9), acteoside (10), and leucosceptoside A (11), two known lignan glucosides, dihydroxymethyl-bis(3,5-dimethoxy-4-hydroxyphenyl) tetrahydrofuran-9 (or 9')-O-beta-glucopyranoside (12) and (+)-lyoniresinol 3alpha-O-beta-D-glucopyranoside (13), a known methyl salicylate glucoside, methyl 2-O-beta-D-glucopyranosylbenzoate (14), and two known sterols, beta-sitosterol 3-O-beta-D-glucopyranoside (15) and beta-sitosterol (16). Their chemical structures were determined on the basis of spectroscopic data. Compound 1 exhibited stronger scavenging effect on the stable free radical 1,1-diphenyl-2-picrylhydrazyl than that of alpha-tocopherol.

Iridoids↗

PubMed2005

The genetics and genomics of the silkworm, Bombyx mori.

We review progress in applying molecular genetic and genomic technologies to studies in the domesticated silkworm, Bombyx mori, highlighting its use as a model for Lepidoptera, and in sericulture and biotechnology. Dense molecular linkage maps are being integrated with classical linkage maps for positional cloning and marker-assisted selection. Classical mutations have been identified by a candidate gene approach. Cytogenetic and sequence analyses show that the W chromosome is composed largely of nested full-length long terminal repeat retrotransposons. Z-chromosome-linked sequences show a lack of dosage compensation. The downstream sex differentiation mechanism has been studied via the silkworm homolog of doublesex. Expressed sequence tagged databases have been used to discover Lepidoptera-specific genes, provide evidence for horizontal gene transfer, and construct microarrays. Physical maps using large-fragment bacterial artificial chromosome libraries have been constructed, and whole-genome shotgun sequencing is underway. Germline transformation and transient expression systems are well established and available for functional studies, high-level protein expression, and gene silencing via RNA interference.

Animals↗

PubMed2004

The genome sequence of silkworm, Bombyx mori.

We performed threefold shotgun sequencing of the silkworm (Bombyx mori) genome to obtain a draft sequence and establish a basic resource for comprehensive genome analysis. By using the newly developed RAMEN assembler, the sequence data derived from whole-genome shotgun (WGS) sequencing were assembled into 49,345 scaffolds that span a total length of 514 Mb including gaps and 387 Mb without gaps. Because the genome size of the silkworm is estimated to be 530 Mb, almost 97% of the genome has been organized in scaffolds, of which 75% has been sequenced. By carrying out a BLAST search for 50 characteristic Bombyx genes and 11,202 non-redundant expressed sequence tags (ESTs) in a Bombyx EST database against the WGS sequence data, we evaluated the validity of the sequence for elucidating the majority of silkworm genes. Analysis of the WGS data revealed that the silkworm genome contains many repetitive sequences with an average length of <500 bp. These repetitive sequences appear to have been derived from truncated transposons, which are interspersed at 2.5- to 3-kb intervals throughout the genome. This pattern suggests that silkworm may have an active mechanism that promotes removal of transposons from the genome. We also found evidence for insertions of mitochondrial DNA fragments at 9 sites. A search for Bombyx orthologs to Drosophila genes controlling sex determination in the WGS data revealed 11 Bombyx genes and suggested that the sex-determining systems differ profoundly between the two species.

Animals↗

PubMed2003

W-derived BAC probes as a new tool for identification of the W chromosome and its aberrations in Bombyx mori.

We isolated four W chromosome-derived bacterial artificial chromosome (W-BAC) clones from Bombyx mori BAC libraries by the polymerase chain reaction and used them as probes for fluorescence in situ hybridization (FISH) on chromosome preparations from B. mori females. All four W-BAC probes surprisingly highlighted the whole wild-type W sex chromosome and also identified the entire original W-chromosomal region in W chromosome-autosome translocation mutants. This is the first successful identification of a single chromosome by means of BAC-FISH in species with holokinetic chromosomes. Genomic in situ hybridization (GISH) by using female-derived genomic probes highlighted the W chromosome in a similar chromosome-painting manner. Besides the W, hybridization signals of W-BAC probes also occurred in telomeric and/or subtelomeric regions of the autosomes. These signals coincided well with those of female genomic probes except one additional GISH signal that was observed in a large heterochromatin block of one autosome pair. Our results support the opinion that the B. mori W chromosome accumulated transposable elements and other repetitive sequences that also occur, but scattered, elsewhere in the respective genome.

Animals↗

PubMed2003

Detachment analysis of the translocated W chromosome shows that the female-specific randomly amplified polymorphic DNA (RAPD) marker, female-218, is derived from the second chromosome fragment region of the translocated W chromosome of the sex-limited p(B) silkworm (Bombyx mori ) strain.

The sex chromosomes of the silkworm, Bombyx mori, are designated ZW for the female and ZZ for the male. We previously characterized a female-specific randomly amplified polymorphic DNA (RAPD) marker, designated Female-218, from the translocation-bearing W chromosomes. These W chromosomes contain a region of the second chromosome, which carries visible larval markers of the p loci. We used strain TWPB in which female larvae have black skin due to the p(B) gene (T(W;2)p(B), +p/+p) while male larvae have whitish skin (+p/+p). To determine whether the Female-218 RAPD marker is derived from the "W region" or a "second chromosome fragment", we induced a detachment of the translocated W chromosome, T(W;2)p(B), by treating the eggs with hot water at an early developmental stage. After hot water treatment, we obtained 27 white female larvae out of 4850 female larvae. The Female-218 RAPD marker was not amplified in 26 out of 27 white female larvae, and was amplified from one white female larva. Moreover, we obtained 11 black male larvae out of 5377 male larvae. Eight out of 11 black male larvae became adult moths, and the Female-218 RAPD marker was amplified from all eight male moths. Examination of the genetic relationship between the Female-218 RAPD marker and the second chromosome fragment of the translocated W chromosome strongly indicates that the Female-218 RAPD marker is amplified from the region of second chromosome fragment of the T(W;2)p(B) chromosome.

Animals↗