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Hachiōji, Japan

Saikusa K.,Yokohama City University | Saikusa K.,Hiroshima University | Shimoyama S.,Yokohama City University | Shimoyama S.,Jasco International Co. | And 7 more authors.
Protein Science

It is well known that various modifications of histone tails play important roles in the regulation of transcription initiation. In this study, some lysine (Lys) and arginine (Arg) residues were acetylated and deiminated, respectively, in the histone H2A/H2B dimer, and charge-neutralization effects on the dimer structure were studied by native mass spectrometry. Given that both acetylation and deimination neutralize the positive charges of basic amino acid residues, it had been expected that these modifications would correspondingly affect the gas-phase behavior of the histone H2A/H2B dimer. Contrary to this expectation, it was found that Arg deimination led to greater difficulty of dissociation of the dimer by gas-phase collision, whereas acetylation of Lys residues did not cause such a drastic change in the dimer stability. In contrast, ion mobility-mass spectrometry (IM-MS) experiments showed that arrival times in the mobility cell both of acetylated and of deiminated dimer ions changed little from those of the unmodified dimer ions, indicating that the sizes of the dimer ions did not change by modification. Charge neutralization of Arg, basicity of which is higher than Lys, might have triggered some alteration of the dimer structure that cannot be found in IM-MS but can be detected by collision in the gas phase. © 2015 The Protein Society. Source

Mitsushio M.,Kagoshima University | Watanabe K.,Kagoshima University | Abe Y.,Kagoshima University | Abe Y.,Jasco International Co. | Higo M.,Kagoshima University
Sensors and Actuators, A: Physical

The response curves and sensor properties of Al-deposited optical fibers with Al film thicknesses of 7-70 nm based on surface plasmon resonance (SPR) were investigated. The response of the Al-deposited optical fiber sensor strongly depends on the thickness of the Al film. Though the sensors with Al show lower sensitivities than those deposited with Au or Ag, the Al-deposited optical fiber sensors have wider refractivity response ranges. The reflection properties of thin (11-31 nm) Al films due to the SPR phenomenon were also measured and considered. The surface characterization of the Al films (15-45 nm) was made by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). The surfaces of these Al films consist of small grains with diameters of 40-80 nm and the surface height distribution is almost random, having a value of more than 8 nm. The XPS analyses showed the presence of native oxide layers with thicknesses of 2-3 nm on the Al films. The Al films having oxide layers with thicknesses of 2-4 nm exhibited no significant change in the sensor properties. The Al-deposited optical fiber sensor also exhibited no change in the sensor properties following prolonged use for 5 months. The response curves of the Al-deposited optical fiber sensors calculated from SPR theoretical equations in consideration of the surface oxide layers, agreed well with those obtained by experimentation. © 2010 Elsevier B.V. All rights reserved. Source

Ieda T.,GERSTEL K.K. | Ochiai N.,GERSTEL K.K. | Miyawaki T.,Jasco International Co. | Ohura T.,Meijo University | Horii Y.,Center for Environmental Science in Saitama
Journal of Chromatography A

A method for the analysis of chlorinated and brominated polycyclic aromatic hydrocarbon (Cl-/Br-PAHs) congeners in environmental samples, such as a soil extract, by comprehensive two-dimensional gas chromatography coupled to a high resolution time-of-flight mass spectrometry (GC×GC-HRTOF-MS) is described. The GC×GC-HRTOF-MS method allowed highly selective group type analysis in the two-dimensional (2D) mass chromatograms with a very narrow mass window (e.g. 0.02Da), accurate mass measurements for the full mass range (m/z 35-600) in GC×GC mode, and the calculation of the elemental composition for the detected Cl-/Br-PAH congeners in the real-world sample. Thirty Cl-/Br-PAHs including higher chlorinated 10 PAHs (e.g. penta, hexa and hepta substitution) and ClBr-PAHs (without analytical standards) were identified with high probability in the soil extract. To our knowledge, highly chlorinated PAHs, such as C14H3Cl7 and C16H3Cl7, and ClBr-PAHs, such as C14H7Cl2Br and C16H8ClBr, were found in the environmental samples for the first time. Other organohalogen compounds; e.g. polychlorinated biphenyls (PCBs), polychlorinated naphthalenes (PCNs), and polychlorinated dibenzofurans (PCDFs) were also detected. This technique provides exhaustive analysis and powerful identification for the unknown and unconfirmed Cl-/Br-PAH congeners in environmental samples. © 2011 Elsevier B.V. Source

Shimoyama S.,Yokohama City University | Shimoyama S.,Jasco International Co. | Nagadoi A.,Yokohama City University | Tachiwana H.,Waseda University | And 5 more authors.
Journal of Mass Spectrometry

Post-translational modifications of histones for reversibly changing chromosomal structures in promoter regions of genes are a prerequisite for transcriptional activation and repression of genes. Peptidylarginine deiminase 4 (PAD4), which mediates histone deimination by converting arginine residues into citrulline residues, is involved in the repression of gene transcription. However, the mechanism is still unclear. We studied the effects of deimination on the reconstituted histone H2A/H2B dimer structure by electrospray ionization mass spectrometry. Deimination of the H2A/H2B dimer by PAD4 indicated that the mass of H2A increased 2.7 Da, suggesting that two or three Arg residues of H2A were deiminated. Deimination of H2A monomer alone showed a 6.6-Da increase in mass. This indicates that about four more Arg residues of H2A are modified in the monomer state than in the H2A/H2B dimer state. Taking account of the finding that the unstructured portions in proteins are susceptible to deimination by PAD4, it is likely that H2A in the monomer state has a more flexible structure than that in the dimer state. Furthermore, analysis of the association of the H2A/H2B dimer in 2 or 4 M ammonium acetate with nano-electrospray ionization mass spectrometry showed that a modified H2A/H2B dimer was less dissociated into H2A and H2B monomers than an unmodified dimer when high voltages were applied to the sample cone. This study provides convincing evidence that PAD4 deimination stabilizes the histone H2A/H2B dimer. Copyright © 2010 John Wiley & Sons, Ltd. Source

Kato K.,Yamagata University | Tokanai F.,Yamagata University | Anshita M.,Yamagata University | Sakurai H.,Yamagata University | Ohashi M.S.,Jasco International Co.

Accelerator mass spectrometry (AMS) was introduced at Yamagata University in 2010, including the measurement of radiocarbon. In the Yamagata University laboratory (YU-AMS), the application of 14C AMS is aimed at microdose pharmacokinetics investigation and the development of improved sample preparation techniques. The lab also measures environmental samples. With the installation of this AMS system, a new automated sample production system was installed, which is composed of an elemental analyzer, a glass vacuum line, and an isotope ratio mass spectrometer (IRMS). In this system, it is also possible to measure stable isotopes (δ13C, δ15N, and δ34S) of the sample gas using a mass spectrometer. To increase the amount of CO2 gas introduced into the glass vacuum line, the gas mass flow introduced into the MS was reduced, and the change of δ13C accompanying this reduction was monitored. The sample gas split was changed to set the glass vacuum line (GVL):isotope ratio mass spectrometer (IRMS) ratio to 5:5, 8:2, and 9:1, and δ13C was measured for each ratio. It was confirmed that there was no effect on the isotopic fractionation accompanying the change in the sample gas split ratio. To prioritize the use of gas in the production of graphite, the GVL:IRMS ratio of 9:1 was chosen for this setup. The components are connected on-line, and up to 20 samples can be processed automatically. © 2014 by the Arizona Board of Regents on behalf of the University of Arizona. Source

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