A5101657692- Genomics and Chromatin Dynamics
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- Click Chemistry and Applications
- Magnetic Field Sensors Techniques
- RNA modifications and cancer
- Magnetic properties of thin films
- Crystallography and molecular interactions
- DNA Repair Mechanisms
- Chromatin Remodeling and Cancer
- Protein Structure and Dynamics
- Mass Spectrometry Techniques and Applications
- Synthesis and Characterization of Heterocyclic Compounds
- Enzyme Structure and Function
- Chemical Synthesis and Analysis
- RNA Research and Splicing
- Neurobiology of Language and Bilingualism
- Atomic and Molecular Physics
- Autophagy in Disease and Therapy
- Dust and Plasma Wave Phenomena
- Biodiesel Production and Applications
- Protein Degradation and Inhibitors
Sumitomo Dainippon Pharma (Japan)
2024
Tokyo University of Science
2022
Aichi Prefectural Nisshin West High School
2022
National Center of Neurology and Psychiatry
2021
Waseda University
2015-2020
University of Yamanashi
2020
Tokushima Municipal High School
2018
Chuo University
2018
Ōtani University
2018
Nagoya City University
2018
Au nanoparticle (AuNP)-embedded carbon films were formed with a one-step reproducible process by using unbalanced magnetron (UBM) cosputtering to make it possible detect As(3+) in water. The sputtered components NPs (typically 5 nm diameter) spontaneously the films, owing poor intermiscibility of carbon. surface contents embedded AuNPs film widely controllable (Au = 13-21 at %) regulating target powers and individually. obtained had flat (Ra 0.1 nm) despite fact partially exposed surface. By...
Nucleosomes are dynamic entities that repositioned along DNA by chromatin remodeling processes. A nucleosome the switch-sucrose nonfermentable (SWI/SNF) remodeler collides with a neighbor and forms intermediate "overlapping dinucleosome." Here, we report crystal structure of overlapping dinucleosome, in which two nucleosomes associated, at 3.14-angstrom resolution. In dinucleosome structure, unusual "hexasome" nucleosome, composed histone hexamer lacking one H2A-H2B dimer from conventional...
Abstract During cellular reprogramming, the pioneer transcription factor GATA3 binds chromatin, and in a context-dependent manner directs local chromatin remodeling enhancer formation. Here, we use high-resolution nucleosome mapping human cells to explore impact of position GATA motifs on surface nucleosomes productive formation, finding productivity correlates with binding sites located near nucleosomal dyad axis. Biochemical experiments model demonstrate sufficiently stable...
Posttranslational modifications (PTMs) of histones play an important role in the complex regulatory mechanisms governing gene transcription, and their dysregulation can cause diseases such as cancer. The lack methods for site-selectively modifying native chromatin, however, limits our understanding functional roles a specific histone PTM, not single mark, but intertwined PTM network. Here, we report synthetic catalyst DMAP-SH (DSH), which activates chemically stable thioesters (including...
An ultrasensitive colorimetric DNA and RNA assay using a combination of enzyme-free click chemical ligation chain reaction (CCLCR) on dispersed gold nanoparticles (GNPs) magnetic separation process has been developed. The between an azide-containing probe DNA-modified GNP dibenzocyclooctyne-containing biotinyl occurred through hybridization with target (RNA) to form the biotinyl-ligated GNPs (ligated products). Eventually, both were amplified exponentially thermal cycling. After...
Abstract SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex, is causative gene rhabdoid tumors and epithelioid sarcomas. Here, we identify paralog pair CBP p300 as synthetic lethal target in SMARCB1-deficient cancers by using dual siRNA screening method based on “simultaneous inhibition pair” concept. Treatment with CBP/p300 inhibitors suppresses growth cell lines tumor xenografts derived from cells but not SMARCB1-proficient cells. SMARCB1-containing complexes localize H3K27me3...
Chromatin structure and gene expression are dynamically regulated by posttranslational modifications of histones. Recent advance in mass spectrometry has identified novel types lysine acylations, such as butyrylation malonylation, whose functions regulations likely different from those acetylation. Sirtuins, nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases, catalyze various deacylations. However, it is poorly understood how distinct sirtuins regulate the acylation...
A new target-responsive DNA strand displacement system via toehold-mediated click chemical ligation was designed and prepared for enzyme-free fluorescent-amplified aptasensors. The aptasensors significantly amplified fluorescent signals in response to targets based on target recycling processes.
Histone tails, which protrude from nucleosome core particles (NCPs), play crucial roles in the regulation of DNA transcription, replication, and repair. In this study, structural diversity nucleosomes was investigated detail by analyzing observed charge states reconstituted with various lengths using positive-mode electrospray ionization mass spectrometry (ESI-MS) molecular dynamics (MD) simulation. Here, we show that canonical NCPs, having 147 bp closely wrapped around a histone octamer,...
An overlapping dinucleosome (OLDN) is a structure composed of one hexasome and octasome appears to be formed through nucleosome collision promoted by remodeling factor(s). In this study, the solution OLDN was investigated integration small-angle x-ray neutron scattering (SAXS SANS, respectively), computer modeling, molecular dynamics simulations. Starting from crystal structure, we generated conformational ensemble based on normal mode analysis searched for conformations that reproduced SAXS...
Inorganic salts and nonvolatile-buffer components affect the structure stability of proteins, some protein complexes are unable to maintain their function without them. However, it is well-known that these cause suppression analyte ionization during electrospray process. Thus, establish appropriate methods for observation intact ions DNA by native mass spectrometry (native MS) in presence nonvolatile buffer components, we herein examined effect ammonium acetate addition a model homotetramer...
The first nucleosomes in the downstream of transcription starting sites are called +1 nucleosomes, which expected to be readily unwrapped for DNA transcription. To investigate accessibility MNase-seq experiments were carried out with 20 reconstituted budding yeast. Although MNase has been known its sequence preference digestions, we confirmed that this is overwhelmed by identifying sequence-driven and accessibility-driven cleavages. Specifically, find sequences favoured at end regions such...
Nuclear autoantigenic sperm proteins (NASPs) are members of the acidic histone chaperones, which promote nucleosome assembly. In humans, two splicing variants proposed for somatic and testicular isoforms, sNASP tNASP, respectively, have been found, shorter form, sNASP, reportedly promotes assembly with H3 H3.1, H3.2, H3.3. However, biochemical properties longer not reported. tNASP is considered to exist specifically in testis. Our present results revealed that protein ubiquitously produced...
This study describes the synthesis of triazine-based dehydrocondensing reagents substituted by amido substituents and demonstrates their efficiency for reactions in MeOH THF. N -Phenylbenzamido-substituted chlorotriazine is readily converted to a stable, non-hygroscopic triazinylammonium-based reagent that superior 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMT-MM) terms its reactivity reactions.
Physiological functions of type 3 ryanodine receptors (RyR3) in smooth muscle (SM) tissues are not well understood, spite their wide expression. However, the short isoform RyR3 is known to be a dominant-negative variant (DN-RyR3), which may negatively regulate both RyR2 and full-length (FL) by forming hetero-tetramers. Here, functional roles regulation Ca2+ signaling mesenteric artery SM cells (MASMCs) were examined using homozygous knockout mice (RyR3-/-). Quantitative PCR analyses...
The structural parameters of ultra-thin zinc oxide films on Rh(100) are investigated using low-energy electron diffraction intensity (LEED I-V) curves, scanning tunneling microscopy (STM), and first-principles density functional theory (DFT) calculations. From the analysis LEED I-V curves DFT calculations, two optimized models A B determined. Their structures basically similar to planer h-BN ZnO(0001) structure, although some oxygen atoms protrude from surface, associated with an in-plane...
Autism spectrum disorders (ASD) are associated with mutations of chromodomain-helicase DNA-binding protein 8 (Chd8) and tuberous sclerosis complex 2 (Tsc2). Although these ASD-related genes detected in glial cells such as microglia, the effect Chd8 or Tsc2 deficiency on microglial functions microglia-mediated brain development remains unclear. In this study, we investigated role cytokine expression, phagocytosis activity, neuro/gliogenesis from neural stem (NSCs) vitro. knockdown microglia...
We present a study using molecular dynamics simulations based on the Fermi–Jagla potential model, which is continuous version of mono-atomic core-softened Jagla model [J. Y. Abraham, S. V. Buldyrev, and N. Giovambattista, J. Phys. Chem. B 115, 14229 (2011)]. This shows water-like liquid-liquid phase transition between high-density low-density liquids at critical point. In particular, slope coexistence line becomes weakly negative, expected to represent one anomalies liquid polyamorphism....
The anomalous volume expansion of poly-(N-isopropyl acrylamide) (PNIPAM) solutions was observed during the thermally induced polymer phase transition aqueous having concentrations in 3-7 wt % range. process occurred on a millisecond time scale, and laser temperature-jump time-resolved technique used to bring about process. After heating solution with pulse exploiting light absorption by dyes added itself, take place, temporal changes associated it were visualized through transient grating...
ABSTRACT This study aimed to investigate how Japanese learners of English as a foreign language, whose first language does not have obligatory morphological number marking, process conceptual plurality. The targeted structure was reciprocal verbs, which require plurality interpret their meanings correctly. results sentence completion task confirmed that participants could use verbs reciprocally in English. In self-paced reading experiment, read sentences with and those optionally transitive...
Gaseous hydrogen selenide (H2Se) generated by the addition of sodium tetrahydroborate (NaBH4) into an acidic aqueous sample was collected using ammonia solution. The selenium (Se) concentration determined graphite furnace atomic absorption spectrometry (AAS). Several experimental conditions, such as type collection solution, volume NaBH4 and hydrochloric acid, time, were optimized. In addition, effect coexisting ions quantitatively evaluated eliminated. limit detection for Se in a standard...