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  • American Physical Society  (13)
  • American Institute of Physics (AIP)  (7)
  • Nature Publishing Group (NPG)  (3)
  • American Physical Society (APS)  (2)
  • 1
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    Phonon drag effect on Seebeck coefficient of ultrathin P-doped Si-on-insulator layers (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-09-10
    Description: The contribution of the phonon drag effect to the Seebeck coefficient of P-doped ultrathin Si-on-insulator (SOI) layers with a thickness of 9–100 nm is investigated for near-room-temperature applications. The contribution is found to be significant in the lightly doped region and to depend on the carrier concentration with increasing carrier concentration above ∼5 × 10 18  cm −3 . Moreover, the contribution is not influenced by SOI thickness above 9 nm. On the basis of phonon mean-free-path calculations considering phonon scattering processes, the phonon drag part of the SOI Seebeck coefficient in the lightly doped region is mainly governed by phonon-phonon scattering. Furthermore, in higher concentration regions, the dependence of phonon drag can be qualitatively explained by the interaction between phonons and doped impurities.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    The nature of the globular- to fibrous-actin transition (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-01-23
    Description: Actin plays crucial parts in cell motility through a dynamic process driven by polymerization and depolymerization, that is, the globular (G) to fibrous (F) actin transition. Although our knowledge about the actin-based cellular functions and the molecules that regulate the G- to F-actin transition is growing, the structural aspects of the transition remain enigmatic. We created a model of F-actin using X-ray fibre diffraction intensities obtained from well oriented sols of rabbit skeletal muscle F-actin to 3.3 A in the radial direction and 5.6 A along the equator. Here we show that the G- to F-actin conformational transition is a simple relative rotation of the two major domains by about 20 degrees. As a result of the domain rotation, the actin molecule in the filament is flat. The flat form is essential for the formation of stable, helical F-actin. Our F-actin structure model provides the basis for understanding actin polymerization as well as its molecular interactions with actin-binding proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oda, Toshiro -- Iwasa, Mitsusada -- Aihara, Tomoki -- Maeda, Yuichiro -- Narita, Akihiro -- England -- Nature. 2009 Jan 22;457(7228):441-5. doi: 10.1038/nature07685.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉X-ray Structural Analysis Research Team, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan. toda@spring8.or.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158791" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/*metabolism ; Animals ; Biopolymers/chemistry/metabolism ; Cell Movement ; Glutamine/metabolism ; Hydrolysis ; Magnetics ; Models, Molecular ; Muscle Contraction ; Muscle, Skeletal/chemistry ; Protein Structure, Quaternary ; Protein Subunits/chemistry/metabolism ; Rabbits ; X-Ray Diffraction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Crystal structure of the human centromeric nucleosome containing CENP-A (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-12
    Description: In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment. Centromeres specify the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A. Although the underlying mechanism is unclear, centromere inheritance is probably dictated by the architecture of the centromeric nucleosome. Here we report the crystal structure of the human centromeric nucleosome containing CENP-A and its cognate alpha-satellite DNA derivative (147 base pairs). In the human CENP-A nucleosome, the DNA is wrapped around the histone octamer, consisting of two each of histones H2A, H2B, H4 and CENP-A, in a left-handed orientation. However, unlike the canonical H3 nucleosome, only the central 121 base pairs of the DNA are visible. The thirteen base pairs from both ends of the DNA are invisible in the crystal structure, and the alphaN helix of CENP-A is shorter than that of H3, which is known to be important for the orientation of the DNA ends in the canonical H3 nucleosome. A structural comparison of the CENP-A and H3 nucleosomes revealed that CENP-A contains two extra amino acid residues (Arg 80 and Gly 81) in the loop 1 region, which is completely exposed to the solvent. Mutations of the CENP-A loop 1 residues reduced CENP-A retention at the centromeres in human cells. Therefore, the CENP-A loop 1 may function in stabilizing the centromeric chromatin containing CENP-A, possibly by providing a binding site for trans-acting factors. The structure provides the first atomic-resolution picture of the centromere-specific nucleosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tachiwana, Hiroaki -- Kagawa, Wataru -- Shiga, Tatsuya -- Osakabe, Akihisa -- Miya, Yuta -- Saito, Kengo -- Hayashi-Takanaka, Yoko -- Oda, Takashi -- Sato, Mamoru -- Park, Sam-Yong -- Kimura, Hiroshi -- Kurumizaka, Hitoshi -- England -- Nature. 2011 Jul 10;476(7359):232-5. doi: 10.1038/nature10258.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21743476" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Autoantigens/*chemistry/metabolism ; Base Sequence ; Chromosomal Proteins, Non-Histone/*chemistry/metabolism ; Crystallography, X-Ray ; DNA/*chemistry/genetics/metabolism ; Histones/*chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Conformation ; Molecular Sequence Data ; Nucleosomes/*chemistry/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Pathogenic exon-trapping by SVA retrotransposon and rescue in Fukuyama muscular dystrophy (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-08
    Description: Fukuyama muscular dystrophy (FCMD; MIM253800), one of the most common autosomal recessive disorders in Japan, was the first human disease found to result from ancestral insertion of a SINE-VNTR-Alu (SVA) retrotransposon into a causative gene. In FCMD, the SVA insertion occurs in the 3' untranslated region (UTR) of the fukutin gene. The pathogenic mechanism for FCMD is unknown, and no effective clinical treatments exist. Here we show that aberrant messenger RNA (mRNA) splicing, induced by SVA exon-trapping, underlies the molecular pathogenesis of FCMD. Quantitative mRNA analysis pinpointed a region that was missing from transcripts in patients with FCMD. This region spans part of the 3' end of the fukutin coding region, a proximal part of the 3' UTR and the SVA insertion. Correspondingly, fukutin mRNA transcripts in patients with FCMD and SVA knock-in model mice were shorter than the expected length. Sequence analysis revealed an abnormal splicing event, provoked by a strong acceptor site in SVA and a rare alternative donor site in fukutin exon 10. The resulting product truncates the fukutin carboxy (C) terminus and adds 129 amino acids encoded by the SVA. Introduction of antisense oligonucleotides (AONs) targeting the splice acceptor, the predicted exonic splicing enhancer and the intronic splicing enhancer prevented pathogenic exon-trapping by SVA in cells of patients with FCMD and model mice, rescuing normal fukutin mRNA expression and protein production. AON treatment also restored fukutin functions, including O-glycosylation of alpha-dystroglycan (alpha-DG) and laminin binding by alpha-DG. Moreover, we observe exon-trapping in other SVA insertions associated with disease (hypercholesterolemia, neutral lipid storage disease) and human-specific SVA insertion in a novel gene. Thus, although splicing into SVA is known, we have discovered in human disease a role for SVA-mediated exon-trapping and demonstrated the promise of splicing modulation therapy as the first radical clinical treatment for FCMD and other SVA-mediated diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412178/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412178/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taniguchi-Ikeda, Mariko -- Kobayashi, Kazuhiro -- Kanagawa, Motoi -- Yu, Chih-chieh -- Mori, Kouhei -- Oda, Tetsuya -- Kuga, Atsushi -- Kurahashi, Hiroki -- Akman, Hasan O -- DiMauro, Salvatore -- Kaji, Ryuji -- Yokota, Toshifumi -- Takeda, Shin'ichi -- Toda, Tatsushi -- T32 AR056993/AR/NIAMS NIH HHS/ -- England -- Nature. 2011 Oct 5;478(7367):127-31. doi: 10.1038/nature10456.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Neurology/Molecular Brain Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21979053" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics ; Alternative Splicing/drug effects/*genetics ; Animals ; Disease Models, Animal ; Dystroglycans/metabolism ; Exons/*genetics ; Gene Knock-In Techniques ; Glycosylation ; Humans ; Introns/genetics ; Japan ; Laminin/metabolism ; Membrane Proteins/genetics/metabolism ; Mice ; Molecular Sequence Data ; Mutagenesis, Insertional/drug effects/genetics ; Oligonucleotides, Antisense/genetics/pharmacology/therapeutic use ; RNA Isoforms/genetics ; RNA Splice Sites/genetics ; Retroelements/*genetics ; Walker-Warburg Syndrome/*genetics/*pathology/therapy
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Pulsed neutron time-dependent intensity modulation for quasi-elastic neutron scattering spectroscopy (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-10-28
    Description: We propose a basic formula and demonstration for a high-resolution quasi-elastic neutron scattering (QENS) by combining the time-of-flight (TOF) method with Modulation of Intensity by Zero Effort (MIEZE) type neutron spin echo spectroscopy. The MIEZE technique has the potential to develop a unique approach to study on slow dynamics of condensed matter; however, the energy resolution is limited owing to the hypersensitivity of the MIEZE signal contrast to the echo condition, which is strongly affected by the alignment of the instruments and the sample. The narrow allowance of the optimal alignment is a major obstacle to the wide use of this technique. Combining the TOF method with MIEZE (TOF-MIEZE), the hypersensitivity of MIEZE signals is significantly alleviated with a short pulsed beam. This robustness is very useful to optimize experimental alignments and enables accurate measurements of QENS. The experimental results demonstrate the characteristic of the TOF-MIEZE technique and are well described by the formula presented in this study.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Published by American Institute of Physics (AIP)
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  • 6
    Electronic Resource
    Electronic Resource
    Stark-effect measurement of high free-electron laser electric fields in MTX by laser-aided particle-probe spectroscopy : Eighth topical conference on high−temperature plasma diagnostics (1990)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 61 (1990), S. 2964-2966 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: We are constructing a diagnostic system to measure the electric field ((approximately-greater-than)100 kV/cm) of a free-electron laser (FEL) beam when injected into the plasma of the Microwave Tokamak Experiment (MTX). The apparatus allows a crossed-beam measurement, with 2 cm spatial resolution in the plasma, involving the FEL beam (with 140 GHz, ≈1 GW ECH pulses), a neutral helium beam, and a dye laser beam. After the laser beam pumps metastable helium atoms to higher excited states, their decay light is detected by an efficient optical system. Because of the Stark effect arising from the FEL electric field (E), a forbidden transition can be strongly induced. The intensity of emitted light resulting from the forbidden transition is proportional to E2. Because photon counting rates are estimated to be low, extra effort is made to minimize background and noise levels. It is possible that the lower E of an MTX gyrotron-produced ECH beam with its longer duration pulses can also be measured using this method. Other applications of the apparatus described here may include measurements of ion temperature (using charge-exchange recombination), edge-density fluctuations, and core impurity concentrations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1141740
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  • 7
    Electronic Resource
    Electronic Resource
    Spectroscopic method to directly measure electric field distribution in tokamak plasma edge : Proceedings of the eleventh topical conference on high temperature plasma diagnostics (1997)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 68 (1997), S. 1028-1031 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: A supersonic helium beam source operated in pulse mode was constructed for direct measurement of electric field distribution in the tokamak plasma edge region with the aid of laser-induced fluorescence (LIF) technique. In this technique only the polarization has to be observed of a LIF resulting from a laser-excited forbidden transition due to the Stark effect and the electric quadrupole to determine the electric field strength. No calibration is needed of the absolute intensity of LIF and tunable laser used. The helium atom beam density was obtained (about 1020 He atoms cm−2 s−1) at a distance of 7 cm from the pulsed nozzle. A model-type experiment to make clear the influence of a magnetic field on the LIF is reported. Design study was also made to install the supersonic beam and spectroscopic measurement system on a medium size tokamak. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1147778
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  • 8
    Electronic Resource
    Electronic Resource
    Measurement of electron density with combined technique of laser blowoff and laser-induced fluorescence (1985)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 56 (1985), S. 1036-1037 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: A method combining the techniques of laser blowoff and laser-induced fluorescence has been developed in order to measure the local electron density below 1013 cm−3. Characteristics of a Li0 beam produced by laser blowoff of a thin Li film are investigated using beam–plasma interactions and laser-induced fluorescence. Such a beam has a near-Maxwellian velocity distribution with a temperature around 4.5 eV and a density of the order of 1010 cm−3 at a distance of about 1 m from the film target. The feasibility of measuring electron density with this Li0 beam and a dye laser is demonstrated with an ECR plasma.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1138260
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  • 9
    Electronic Resource
    Electronic Resource
    Polarized laser-induced fluorescence spectroscopy for measuring electric field distribution in plasmas : Proceedings of the 12th topical conference on high temperature plasma diagnostics (1999)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 70 (1999), S. 903-907 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: A sensitive and reliable spectroscopic system measuring simultaneously polarized components of time-resolved laser induced fluorescence (LIF) is being developed for determining electric field distribution in transient plasmas under strong magnetic field. In this LIF method which we have already proposed, only the polarization has to be observed of a LIF due to a laser-excited forbidden transition caused by both the Stark effect and the electric quadrupole (QDP) moment in the plasmas. Temporal evolution of both the polarized LIF components is simultaneously observed using a Glan–Thompson polarizing beamsplitter with extinction ratio of 10−5 and a pair of photomultipliers with fast rise time. The polarization components observed in a hollow cathode discharge He plasma under magnetic field of 2.5 kG were successfully analyzed and electric field distribution in the sheath region was accurately estimated using this procedure. It was also shown that electric field strength was determined from the intensity ratio of the Stark and QDP components separated in the strong magnetic field. We briefly discuss the applicability of this spectroscopic system to diagnostic in the edge region of tokamak plasmas. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1149447
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  • 10
    Electronic Resource
    Electronic Resource
    Development of Li beam probing and laser-induced fluorescence technique for electric field measurement in a plasma (1988)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 59 (1988), S. 2351-2356 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: To measure local electric field in an rf-plugged sheet plasma in the RFC-XX-M open-ended machine, a spectroscopic system using a combined technique of Li-beam probing (laser blow-off method) and laser-induced fluorescence has been developed. A Li atom in the rf field can be populated to 42F by a stepwise laser pumping (22S→22P→42F) because of the Stark mixing between 42F and 42D. A cascade fluorescence of 610.4 nm (32D→22P) subsequent to the direct transition (42F→32D) was observed to estimate the rf field strength (rms) Erms. To correct the effect of electron collisions in the plasma, we observed a blue fluorescence consisting of two lines: a forbidden line of 460.2 nm (42F→22P) and an allowed line of 460.3 nm (42D→22P) induced by electron collisional transfer (42F→42D). From these intensities, we obtained Erms and electron density ne by solving numerically the rate equations, including the relevant radiative and collisional processes under the experimental conditions. Erms and ne were estimated to be 2.4 kV/cm and 3.1×1011 cm−3 near the center of the sheet plasma, respectively. It was found that the obtained Erms was enhanced by about 2.5 times with respect to the vacuum field (1 kV/cm). The obtained ne agreed well with ones by other methods. A spatial distribution of ne was also obtained from that of the Li0 resonance line (22P→22S) due to electron impact excitation. The present spectroscopic system is applicable to plasmas of ne(approximately-less-than)1013 cm−3 and static or quasi-static electric fields of E(approximately-greater-than)400 V/cm.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1139960
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