Mb-level CpG and TFBS islands visualized by AI and their roles in the nuclear organization of the human genome.

Unsupervised machine learning that can discover novel knowledge from big sequence data without prior knowledge or particular models is highly desirable for current genome study. We previously established a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions, which can reveal various novel genome characteristics from big sequence data, and found that transcription factor binding sequences (TFBSs) and CpG-containing oligonucleotides are enriched in human centromeric and pericentromeric regions, which support centromere clustering and form the condensed heterochromatin "chromocenter" in interphase nuclei. The number and size of chromocenters, as well as the type of centromeres gathered in individual chromocenters, vary depending on cell type.

Circulating S100A8/A9 is potentially a biomarker that could reflect the severity of experimental colitis in rats.

Aims: The clinical significance of circulating S100A8/A9 (calprotectin) in patients with ulcerative colitis (UC) is poorly understood. We examined whether serum S100A8/A9 is a good biomarker for UC, and whether the serum level is a useful index for the severity of the disease.

Main Methods: Experimental animal (rats) were used to verify clinical significance of serum S100A8/A9 as a biomarker.

Effect of Polycyclic Aromatic Hydrocarbons on Development of the Ascidian Type A.

Polycyclic aromatic hydrocarbons (PAHs) are pollutants that exert harmful effects on marine invertebrates; however, the molecular mechanism underlying PAH action remains unclear. We investigated the effect of PAHs on the ascidian type A (). First, the influence of PAHs on early development was evaluated.

Generation of Schubert polynomial series via nanometre-scale photoisomerization in photochromic single crystal and double-probe optical near-field measurements.

Generation of irregular time series based on physical processes is indispensable in computing and artificial intelligence. In this report, we propose and demonstrate the generation of Schubert polynomials, which are the foundation of versatile permutations in mathematics, via optical near-field processes introduced in a photochromic crystal of diarylethene combined with a simple photon detection protocol. Optical near-field excitation on the surface of a photochromic single crystal yields a chain of local photoisomerization, forming a complex pattern on the opposite side of the crystal.

Exceptional Enlargement of the Mitochondrial Genome Results from Distinct Causes in Different Rain Frogs (Anura: Brevicipitidae: ).

The mitochondrial (mt) genome of the bushveld rain frog (, Brevicipitidae, Afrobatrachia) is the largest (28.8 kbp) among the vertebrates investigated to date. The major cause of genome size enlargement in this species is the duplication of multiple genomic regions.

Pediludiella daitoensis gen. et sp. nov. (Scenedesmaceae, Chlorophyceae), a large coccoid green alga isolated from a Loxodes ciliate.

Freshwater protists often harbor unicellular green algae within their cells. In ciliates, possibly because of large host cell sizes and the small size of algal coccoids, a single host cell typically contains more than a hundred algal cells. While surveying such algae-bearing protists on Minami Daito Jima Island in Japan, we found a green Loxodes ciliate (Loxodida, Karyorelictea) that contained one or two dozens of very large coccoid algae.

Metagenome Sequences from the Environment of Diseased Otter Clams, Lutraria rhynchaena, from a Farm in Vietnam.

Otter clam farming in Vietnam has recently encountered difficulties due to swollen-siphon disease. Here, we report the metagenome sequences of microorganisms extracted from the siphon tissue of infected otter clams. The data comprised bacterial and viral sequences which likely include those derived from the disease-causing agent.

Nuclear magnetic resonance spectroscopy and mass spectrometry data for sulfated isoguanine glycosides.

The data presented here are related to the research paper entitled "Rare sulfated purine alkaloid glycosides from pupal case" [1]. In this data article, we provide 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and electrospray ionization mass spectrometry (ESIMS) data of three undescribed sulfated purine alkaloids, locustoside A disulfate, saikachinoside B disulfate, and saikachinoside A trisulfate isolated from the pupal case of the wild bruchid seed beetle (Chrysomelidae, Bruchinae) infesting the seed of Miquel (Fabaceae).

NMR and ESIMS data for bisabolane-type sesquiterpenoids.

The data presented here are related to the research paper entitled "Norbisabolane and bisabolane sesquiterpenoids from the seeds of " [1]. In this data article, we provide 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and electrospray ionization mass spectrometry (ESIMS) data of three undescribed norbisabolane- and bisabolene-type sesquiterpenoids, ashitabaol B-D isolated from the seeds of .

Cyclin-dependent kinase Pho85p and its cyclins are involved in replicative lifespan through multiple pathways in yeast.

Lifespan is determined by genetic factors and influenced by environmental factors. Here, we find that the phosphate signal transduction (PHO) pathway is involved in the determination of replicative lifespan in budding yeast. Extracellular phosphate does not affect the lifespan.

Acorbine, a Corbicula japonica-derived tripeptide containing non-proteinogenic amino acids, suppresses ethanol-induced liver injury.

Since ancient times, Corbicula extract has been believed in Japan to have hepatoprotective effects, but it remains unclear whether these claims are true, and if so, which component is responsible for hepatoprotection. In this study, we showed that Corbicula extract exerted a protective effect against liver damage. Recent work identified acorbine (β-alanyl-ornithyl-ornithine), a novel tripeptide containing non-proteinogenic amino acids, in the extract of Corbicula japonica.

Curcumin Derivatives Verify the Essentiality of ROS Upregulation in Tumor Suppression.

Background: Curcumin has been shown to exert pleiotropic biological effects, including anti-tumorigenic activity. We previously showed that curcumin controls reactive oxygen species (ROS) levels through the ROS metabolic enzymes, to prevent tumor cell growth. In this study, we synthesized 39 novel curcumin derivatives and examined their anti-proliferative and anti-tumorigenic properties.

Unique high sensitivity to heat of axolotl TRPV1 revealed by the heterologous expression system.

The thermosensation mechanism plays critical roles in various animals living in different thermal environment. We focused on an axolotl, which is a tailed amphibian originally from Lake Xochimilco area in the Vally of Mexico, and examined its behavior response to heat stimulation. Mild heat at 33 °C induced noxious locomotive activity to axolotls, but the noxious response of another tailed amphibian, Iberian ribbed newt, was not observed at 33 °C.

Respirovirus C protein inhibits activation of type I interferon receptor-associated kinases to block JAK-STAT signaling.

Respirovirus C protein blocks the type I interferon (IFN)-stimulated activation of the JAK-STAT pathway. It has been reported that C protein inhibits IFN-α-stimulated tyrosine phosphorylation of STATs, but the underlying mechanism is poorly understood. Here, we show that the C protein of Sendai virus (SeV), a member of the Respirovirus genus, binds to the IFN receptor subunit IFN-α/β receptor subunit (IFNAR)2 and inhibits IFN-α-stimulated tyrosine phosphorylation of the upstream receptor-associated kinases, JAK1 and TYK2.

Molecular identification of biwa trout () using PCR-RFLP method.

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was used to identify meat from biwa trout (), amago trout (), yamame trout (), and rainbow trout (). PCR amplification was conducted using primers flanking conserved regions of NADH dehydrogenase subunits 4 and 5 (ND4-ND5) (2848 bp) and ND1 (1091 bp) genes of mitochondrial DNA following restriction digestion with the enzyme III. Although the segments of ND4-ND5 and ND1 genes showed intraspecies variation, the generation of DNA fragments larger than 300 bp and 160 bp following cleavage by HaeIII of ND4-ND5 and ND1, respectively, was efficient to differentiate the four species.

Proline metabolism regulates replicative lifespan in the yeast .

In many plants and microorganisms, intracellular proline has a protective role against various stresses, including heat-shock, oxidation and osmolarity. Environmental stresses induce cellular senescence in a variety of eukaryotes. Here we showed that intracellular proline regulates the replicative lifespan in the budding yeast .

Pentagamavunon-1 (PGV-1) inhibits ROS metabolic enzymes and suppresses tumor cell growth by inducing M phase (prometaphase) arrest and cell senescence.

We previously showed that curcumin, a phytopolyphenol found in turmeric (Curcuma longa), targets a series of enzymes in the ROS metabolic pathway, induces irreversible growth arrest, and causes apoptosis. In this study, we tested Pentagamavunon-1 (PGV-1), a molecule related to curcumin, for its inhibitory activity on tumor cells in vitro and in vivo. PGV-1 exhibited 60 times lower GI compared to that of curcumin in K562 cells, and inhibited the proliferation of cell lines derived from leukemia, breast adenocarcinoma, cervical cancer, uterine cancer, and pancreatic cancer.

Charge transfer dynamics in chlorophyll-based biosolar cells.

We fabricated a chlorophyll (Chl)-based biosolar cell with HChl-sensitized TiO as an acceptor and (ZnChl) as a donor. This solar cell gives a relatively high quantum yield from the absorption spectral contribution from both the donor and acceptor species. We employed subpicosecond time-resolved absorption spectroscopy (TAS) to study the excited state dynamics at the Chl interface.

Drosophila melanogaster as a model for understanding polyADP-ribosylation.

PolyADP-ribosylation is a post-translational modification which is involved in various physiological processes including maintenance of genome stability through DNA repair, regulation of transcription, and development. This process is also involved in pathological events such as cell death. Here, we review the effect of polyADP-ribosylation in signal transduction pathways in system.

Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka .

Medaka ( sp.) is an important fish species in ecotoxicology and considered as a model species due to its biological features including small body size and short generation time. Since Japanese medaka is a freshwater species with access to an excellent genome resource, the marine medaka is also applicable for the marine ecotoxicology.

Entangled-photon decision maker.

The competitive multi-armed bandit (CMAB) problem is related to social issues such as maximizing total social benefits while preserving equality among individuals by overcoming conflicts between individual decisions, which could seriously decrease social benefits. The study described herein provides experimental evidence that entangled photons physically resolve the CMAB in the 2-arms 2-players case, maximizing the social rewards while ensuring equality. Moreover, we demonstrated that deception, or outperforming the other player by receiving a greater reward, cannot be accomplished in a polarization-entangled-photon-based system, while deception is achievable in systems based on classical polarization-correlated photons with fixed polarizations.

Conflicting effects of poly(ADP-ribose) polymerase inhibitor on cell-mediated and virion-mediated HTLV-1 infection.

Adult T-cell leukemia and human T-cell leukemia virus type 1 (HTLV-1) - associated myelopathy/tropical spastic paraparesis, which develop after HTLV-1 infection, are difficult to cure. In particular, the mode of HTLV-1 propagation is not well understood. Poly (ADP-ribose) polymerase-1 is reported to be a co-activator of HTLV-1 Tax protein; however, the effects of polyADP-ribosylation on infectivity of HTLV-1 have not been fully clarified.

Vertebrates originally possess four functional subtypes of G protein-coupled melatonin receptor.

Melatonin receptors (MTNRs) belonging to the G protein-coupled receptor family are considered to consist of three subtypes in vertebrates: MTNR1a, MTNR1b and MTNR1c. Additionally, MTNR1a-like genes have been identified in teleostean species as a fish-specific subtype of MTNR1a. However, similar molecules to this MTNR1a-like gene can be found in some reptiles upon searching the DNA database.