A5047997748- DNA and Nucleic Acid Chemistry
- DNA Repair Mechanisms
- Advanced biosensing and bioanalysis techniques
- Genomics and Chromatin Dynamics
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- RNA Interference and Gene Delivery
- Bacteriophages and microbial interactions
- Electron and X-Ray Spectroscopy Techniques
- Integrated Circuits and Semiconductor Failure Analysis
- Adipose Tissue and Metabolism
- Epigenetics and DNA Methylation
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Carcinogens and Genotoxicity Assessment
- RNA modifications and cancer
- Escherichia coli research studies
- Cancer therapeutics and mechanisms
- Advanced Biosensing Techniques and Applications
- RNA Research and Splicing
- ATP Synthase and ATPases Research
- CRISPR and Genetic Engineering
- Chromatin Remodeling and Cancer
- Biotin and Related Studies
- Mitochondrial Function and Pathology
Yokohama City University
2004-2024
RIKEN Center for Integrative Medical Sciences
2021-2024
Tokyo Institute of Technology
2020-2021
Samsung (South Korea)
2009-2017
Kyoto University
2009-2016
National Institute of Diabetes and Digestive and Kidney Diseases
2013
Japan Science and Technology Agency
2013
National Institutes of Health
2010-2013
Material Sciences (United States)
2009
Tokyo Metropolitan Police Department
2006-2007
Adenosine 5′-triphosphate (ATP) is the major energy currency of all living organisms. Despite its important functions, spatiotemporal dynamics ATP levels inside multicellular organisms unclear. In this study, we modified genetically encoded Förster resonance transfer (FRET)-based biosensor ATeam to optimize affinity at low temperatures. This new biosensor, AT1.03NL, detected changes Drosophila S2 cells more sensitively than original did, 25 °C. By expressing AT1.03NL in melanogaster and...
Abstract The distribution of sarcomeric myosin heavy chain (MyHC) has been examined immunoctochemically in the presumptive myocardial cells chicken embryos (stages 6–10) prior to onset heart beat. Embryos were stained with monoclonal antibody MF20, a reagent which recognizes all MyHCs (Bader et al., 1982), and then both whole mount by immunofluorescence semithin, plastic‐embedded sections following immunoperoxidase labeling. We observed that could be detected as early stage 7 (0–2 pairs...
Significance In plants, RNA-induced silencing complexes that contain 22-nucleotide small interfering RNA (siRNA) and Argonaute 1 protein induce siRNA amplification from their targets. this pathway, double-stranded RNAs (dsRNAs) are synthesized by RNA-dependent polymerase proteins, the dsRNAs processed into siRNAs Dicer-like leading to of Because dsRNA formation nontarget causes nonspecific production, pathway needs be strictly regulated. By using an in vitro system, we demonstrate proteins...
Significance DNA transposons move from one genomic location to another using a transposase. A regulatory protein might assist in target selection and avoiding self-destruction. MuB is the of Mu transposon. Here we report that an AAA+ (ATPase associated with diverse cellular activities) ATPase forms right-handed helical filaments around DNA. The parameters are mismatched their interactions nonuniform. We propose enhanced ATP hydrolysis by MuB, induced contacts MuA-transposon-end complex,...
Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites gene expression in both physiological pathological states. However, such studies have been difficult to establish vivo as a result absence suitable imaging methods. Here, we describe high-resolution fluorescence method, ECHO-liveFISH, label endogenous living mice chicks. Upon electroporation, exciton-controlled sequence-specific oligonucleotide probes revealed...
The Escherichia coli RuvA and RuvB protein complex promotes branch migration of Holliday junctions during recombinational repair homologous recombination at stalled replication forks. belongs to the AAA + (ATPase associated with various cellular activities) ATPase family forms a hexameric ring in an ATP-dependent manner. Studies on oligomeric class ATPases suggest that conserved arginine residue is located close proximity site adjacent subunit plays essential role ATP hydrolysis. This study...
N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im 1-5 different number of Im rings were synthesized, their binding behaviour was investigated surface plasmon resonance assay. It found association rate (k(a)) the target decreased in polyamides. The structures four-ring derived from density functional theory revealed dihedral...
N-Methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that can recognize predetermined DNA sequences with high sequence specificity. As many eukaryotic promoter regions contain highly GC-rich sequences, it is valuable to synthesize and characterize Py-Im motifs. In this study, we synthesized four hairpin 1-4, which 5'-GCGC-3' investigated their binding behavior surface plasmon resonance assay. 2-4 two, one, one β-alanine units, replacing the Py units of 1,...
Abstract Polycomb group proteins (PcG), polycomb repressive complexes 1 and 2 (PRC1 2), repress lineage inappropriate genes during development to maintain proper cellular identities. It has been recognized that PRC1 localizes at the replication fork, however, precise functions of DNA are elusive. Here, we reveal a variant containing PCGF1 (PCGF1-PRC1) prevents overloading activators chromatin remodeling factors on nascent thereby mediates deposition nucleosomes correct downstream...
The Escherichia coli RuvA-RuvB complex promotes branch migration of Holliday junction DNA, which is the central intermediate homologous recombination. Like many DNA motor proteins, it suggested that by driving helical rotation DNA. To clarify RuvA-RuvB-mediated mechanism in more detail, we observed during attaching a bead to one end cruciform was fixed glass surface at opposite end. Bead when RuvA, RuvB, and ATP were added solution. We measured rotational rates beads caused various...
Sequence-specific DNA-binding modules, N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamides have been recently conjugated with fluorophores, and some of these conjugates could be used for the detection specific DNA sequences. In this study, we synthesized two Py-Im 1 2, which interact 145-bp nucleosome positioning sequence 601. We cyanine dye Cy3 or Cy5 2. absence target DNA, fluorescent conjugate a polyamide had lower fluorescence intensity compared alone. presence either nucleosome,...
Abstract The Escherichia coli RuvB hexameric ring motor proteins, together with RuvAs, promote branch migration of Holliday junction DNA. Zero mode waveguides (ZMWs) constitute nanosized holes and enable the visualization a single fluorescent molecule under micromolar order molecules, which is applicable to characterize formation RuvA–RuvB–Holliday DNA complex. In this study, we used ZMWs counted number RuvBs binding RuvA–Holliday Our data demonstrated that different nucleotide analogs...
Abstract Mapping protein interaction complexes in their natural state vivo is arguably the Holy Grail of network analysis. Detection stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe development HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for discovery. The approach enables rapid capture newly expressed...
Fluorescent conjugates of Py–Im polyamides are used as sequence-specific fluorescent probes and applied to the characterisation protein–DNA complex dynamics.
Defect localization of short failures has been a big challenge in modern advanced nanoscale devices. In recent years, Electron Beam Induced Resistance Change (EBIRCh) technique applied to failure analysis. The EBIRCh incorporated into SEM based nanoprobing system allows not only direct electrical characterization suspicious bridge sites but also pinpointing defects with resolution. this paper, we directly measure electron beam induced current variations nanoprober for comprehensive...
The draft genome sequence of the deep-sea yeast Naganishia liquefaciens strain N6, isolated from Japan Trench, is reported here. This was previously classified into a Cryptococcus clade. Phylogenetic analysis using presented suggests that N6 in clade genus Naganishia.
The SRP (Samsung Reconfigurable Processor) is a high-performance, low-power digital signal processor that supports two different operating modes: the VLIW (very long instruction word) mode for running control-intensive code and CGA (coarse-grained reconfigurable array) computation-intensive code. In SRP, an application starts in mode, then may switch back forth many times between throughout its lifetime. order to support this switching seamlessly, our C compiler capable of generating...
Abstract This paper presents the process of measuring static noise margin (SNM), write (WNM) with 6 pin nanoprober, and characterization analysis SRAM cell stability through case studies 45nm devices soft failures. It highlights that local mismatch in bit caused by slight variations transistor characteristics, such as Vth shift Idsat, off variation, also can easily induce a failure. The SNM TR characteristic is successfully demonstrated study devices. chapter explains measurement metal layer...
We have reported successful reconstitution of bacteriorhodopsin (bR) into novel partially fluorinated phosphatidylcholine (diF4H10-PC) vesicles, in that the reconstituted bR has native-like higher order structure and photocycle.The present study on structural stability demonstrated 2D crystals as well trimeric molecules are maintained no light-induced denaturation is observed up to ~40 °C, which much than gel-to-liquid crystalline phase transition temperature (5 °C) pure diF4H10-PC...
We have reported successful reconstitution of bacteriorhodopsin (bR) into novel partially fluorinated phosphatidylcholine (diF4H10-PC) vesicles, in that the reconstituted bR has native-like higher order structure and photocycle.The present study on structural stability demonstrated 2D crystals as well trimeric molecules are maintained no light-induced denaturation is observed up to ~40 °C, which much than gel-to-liquid crystalline phase transition temperature (5 °C) pure diF4H10-PC...