Hidehiro Toh
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View article: Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes
Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes Open
Ancient evolutionary transitions in animal chromosomal complements and their phenotypic impacts remain understudied. Few systems exist where these events can be dissected into individual steps. In coleoid cephalopods (octopus, squid, cuttl…
View article: Chromosome-level genome assembly of the gerbera (<i>Gerbera hybrida</i>) using HiFi long-read and Hi-C technologies
Chromosome-level genome assembly of the gerbera (<i>Gerbera hybrida</i>) using HiFi long-read and Hi-C technologies Open
Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida , which wa…
View article: Genomic characterization of two <i>Faecalibacterium</i> strains isolated from a healthy Japanese individual
Genomic characterization of two <i>Faecalibacterium</i> strains isolated from a healthy Japanese individual Open
The genome sequences of two Faecalibacterium strains isolated from a healthy Japanese individual were analyzed. Comparative genomics revealed the smallest genome within the genus to date and identified core gene clusters, providing new ins…
View article: Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes
Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes Open
Why some animal groups retain ancestral chromosomal complements while others change significantly is a fundamental question in evolutionary genomics. Few systems exist where accumulations of chromosomal changes can be studied in the contex…
View article: A deletion at the X-linked<i>ARHGAP36</i>gene locus is associated with the orange coloration of tortoiseshell and calico cats
A deletion at the X-linked<i>ARHGAP36</i>gene locus is associated with the orange coloration of tortoiseshell and calico cats Open
The X-linked orange ( O ) locus in domestic cats controls an unknown molecular mechanism that causes the suppression of black-brownish pigmentation in favor of orange coloration. The alternating black-brownish and orange patches seen in to…
View article: Epigenetic dynamics of partially methylated domains in human placenta and trophoblast stem cells
Epigenetic dynamics of partially methylated domains in human placenta and trophoblast stem cells Open
Our findings suggest that spatiotemporal genomic features shape megabase-scale DNA methylation patterns, including PMDs, in the human placenta and highlight distinct differences in PMDs between human cytotrophoblasts and trophoblast stem c…
View article: Cholesterol sulfate prevents maternal–fetal conflict by locally modulating immune reactivity
Cholesterol sulfate prevents maternal–fetal conflict by locally modulating immune reactivity Open
Although placental mammals are at high risk of maternal–fetal immune conflict, it is unclear how the semi-allogeneic fetus avoids rejection. Cholesterol sulfate (CS) is a bioactive metabolite that inhibits leukocyte migration and activatio…
View article: Mitochondrial phylogeny and distribution of cytoplasmic male sterility-associated genes in Beta vulgaris
Mitochondrial phylogeny and distribution of cytoplasmic male sterility-associated genes in Beta vulgaris Open
Cytoplasmic male sterility (CMS) is a mitochondrial-encoded trait that confers reproductive defects in males but not in females or any vegetative function. Why CMS is so often found in plants should be investigated from the viewpoint of mi…
View article: A Novel C-Terminal Truncated Bacteriocin Found by Comparison between Leuconostoc mesenteroides 406 and 213M0 Isolated from Mongolian Traditional Fermented Milk, Airag
A Novel C-Terminal Truncated Bacteriocin Found by Comparison between Leuconostoc mesenteroides 406 and 213M0 Isolated from Mongolian Traditional Fermented Milk, Airag Open
Bacteriocins produced by lactic acid bacteria are known to be useful tools for food biopreservation and fermentation control. Leuconostoc mesenteroides subsp. mesenteroides 406 and 213M0 isolated from different samples of Mongolian traditi…
View article: Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes
Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes Open
DNA methylation is an essential epigenetic mechanism that regulates cellular reprogramming and development. Studies using whole-genome bisulfite sequencing have revealed distinct DNA methylome landscapes in human and mouse cells and tissue…
View article: The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes
The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes Open
Establishment of a proper DNA methylation landscape in mammalian oocytes is important for maternal imprinting and embryonic development. De novo DNA methylation in oocytes is mediated by the DNA methyltransferase DNMT3A, which has an ATRX-…
View article: Isolation and genomic analysis of a type IV pili-independent <i>Thermus thermophilus</i> phage, φMN1 from a Japanese hot spring
Isolation and genomic analysis of a type IV pili-independent <i>Thermus thermophilus</i> phage, φMN1 from a Japanese hot spring Open
A Thermus thermophilus lytic phage was isolated from a Japanese hot spring using a type IV pili-deficient strain as an indicator host, and designated as φMN1. Electron microscopic (EM) examination revealed that φMN1 had an icosahedral head…
View article: CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers Open
Background Epigenetic modifications established in mammalian gametes are largely reprogrammed during early development, however, are partly inherited by the embryo to support its development. In this study, we examine CpG island (CGI) sequ…
View article: The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes
The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes Open
DNA methylation at CG sites is important for gene regulation and embryonic development. In mouse oocytes, de novo CG methylation requires preceding transcription-coupled histone mark H3K36me3 and is mediated by a DNA methyltransferase DNMT…
View article: Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation
Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation Open
Because spermatogonial stem cells (SSCs) are immortal by serial transplantation, SSC aging in intact testes is considered to be caused by a deteriorated microenvironment. Here, we report a cell-intrinsic mode of SSC aging by glycolysis act…
View article: Draft Genome Sequence of Butyricimonas faecihominis 30A1, Isolated from Feces of a Japanese Alzheimer’s Disease Patient
Draft Genome Sequence of Butyricimonas faecihominis 30A1, Isolated from Feces of a Japanese Alzheimer’s Disease Patient Open
Butyricimonas faecihominis 30A1, a butyrate-producing bacterium, was isolated from feces of a Japanese Alzheimer’s disease patient. Here, we report the draft genome sequence of this organism.
View article: Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos
Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos Open
The methylation of cytosine at CG sites in the mammalian genome is dynamically reprogrammed during gametogenesis and preimplantation development. It was previously shown that oocyte-derived DNMT1 (a maintenance methyltransferase) is essent…
View article: Draft Genome Sequence of Bifidobacterium lemurum DSM 28807 <sup>T</sup> Isolated from the Gastrointestinal Tracts of Ring-Tailed Lemurs ( <i>Lemur catta</i> )
Draft Genome Sequence of Bifidobacterium lemurum DSM 28807 <sup>T</sup> Isolated from the Gastrointestinal Tracts of Ring-Tailed Lemurs ( <i>Lemur catta</i> ) Open
Bifidobacterium lemurum DSM 28807 T was isolated from the gastrointestinal tracts of ring-tailed lemurs ( Lemur catta ). Here, we report the first draft genome sequence of this organism.
View article: Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes
Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes Open
The mouse PIWI-interacting RNA (piRNA) pathway produces a class of 26-30-nucleotide (nt) small RNAs and is essential for spermatogenesis and retrotransposon repression. In oocytes, however, its regulation and function are poorly understood…
View article: Draft Genome Sequence of Probiotic Lactobacillus acidophilus Strain L-55 Isolated from a Healthy Human Gut
Draft Genome Sequence of Probiotic Lactobacillus acidophilus Strain L-55 Isolated from a Healthy Human Gut Open
Probiotic Lactobacillus acidophilus L-55 was isolated from a healthy human gut. Here, we report the draft genome sequence of this organism.
View article: Draft Genome Sequence of <i>Leuconostoc mesenteroides</i> 213M0, Isolated from Traditional Fermented Mare Milk Airag in Bulgan Aimag, Mongolia
Draft Genome Sequence of <i>Leuconostoc mesenteroides</i> 213M0, Isolated from Traditional Fermented Mare Milk Airag in Bulgan Aimag, Mongolia Open
Leuconostoc mesenteroides 213M0 was isolated from traditional fermented mare milk airag in Bulgan Aimag, Mongolia. This strain produces a listericidal bacteriocin-like inhibitory substance. Here, we report the draft genome sequence of this…
View article: Draft Genome Sequence of <i>Leuconostoc mesenteroides</i> 406 Isolated from the Traditional Fermented Mare Milk Airag in Tuv Aimag, Mongolia
Draft Genome Sequence of <i>Leuconostoc mesenteroides</i> 406 Isolated from the Traditional Fermented Mare Milk Airag in Tuv Aimag, Mongolia Open
Leuconostoc mesenteroides 406 was isolated from the traditional fermented mare milk airag in Tuv Aimag, Mongolia. This strain produces an antilisterial bacteriocin. Here, we report the draft genome sequence of this organism.
View article: Draft Genome Sequence of Coccoid Lactobacillus equigenerosi NRIC 0697 <sup>T</sup> Isolated from the Gastrointestinal Tracts of Healthy Thoroughbreds
Draft Genome Sequence of Coccoid Lactobacillus equigenerosi NRIC 0697 <sup>T</sup> Isolated from the Gastrointestinal Tracts of Healthy Thoroughbreds Open
Lactobacillus equi generosi NRIC 0697 T was isolated from the gastrointestinal tracts of healthy thoroughbreds. This strain produced unique spherical or oval cells, which is rare in the genus Lactobacillus . Here, we report the draft genom…
View article: Draft Genome Sequence of Streptococcus orisasini SH06, Isolated from a Healthy Thoroughbred Gastrointestinal Tract
Draft Genome Sequence of Streptococcus orisasini SH06, Isolated from a Healthy Thoroughbred Gastrointestinal Tract Open
Streptococcus orisasini SH06 was isolated from a healthy thoroughbred gastrointestinal tract. Here, we report the draft genome sequence of this organism. This paper is the first published report of the genomic sequence of S. orisasini .