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8. Definition of the immune evasion-replication interface of rabies virus P protein

Author

Schnell, MJ, Zhan, J, Harrison, AR, Portelli, S, Nguyen, TB, Kojima, I, Zheng, S, Yan, F, Masatani, T, Rawlinson, SM, Sethi, A, Ito, N, Ascher, DB, Moseley, GW, Gooley, PR, Schnell, MJ, Zhan, J, Harrison, AR, Portelli, S, Nguyen, TB, Kojima, I, Zheng, S, Yan, F, Masatani, T, Rawlinson, SM, Sethi, A, Ito, N, Ascher, DB, Moseley, GW, and Gooley, PR

Abstract

Rabies virus phosphoprotein (P protein) is a multifunctional protein that plays key roles in replication as the polymerase cofactor that binds to the complex of viral genomic RNA and the nucleoprotein (N protein), and in evading the innate immune response by binding to STAT transcription factors. These interactions are mediated by the C-terminal domain of P (PCTD). The colocation of these binding sites in the small globular PCTD raises the question of how these interactions underlying replication and immune evasion, central to viral infection, are coordinated and, potentially, coregulated. While direct data on the binding interface of the PCTD for STAT1 is available, the lack of direct structural data on the sites that bind N protein limits our understanding of this interaction hub. The PCTD was proposed to bind via two sites to a flexible loop of N protein (Npep) that is not visible in crystal structures, but no direct analysis of this interaction has been reported. Here we use Nuclear Magnetic Resonance, and molecular modelling to show N protein residues, Leu381, Asp383, Asp384 and phosphor-Ser389, are likely to bind to a 'positive patch' of the PCTD formed by Lys211, Lys214 and Arg260. Furthermore, in contrast to previous predictions we identify a single site of interaction on the PCTD by this Npep. Intriguingly, this site is proximal to the defined STAT1 binding site that includes Ile201 to Phe209. However, cell-based assays indicate that STAT1 and N protein do not compete for P protein. Thus, it appears that interactions critical to replication and immune evasion can occur simultaneously with the same molecules of P protein so that the binding of P protein to activated STAT1 can potentially occur without interrupting interactions involved in replication. These data suggest that replication complexes might be directly involved in STAT1 antagonism.

Published
2021

25. Surface evolution of ultrahigh vacuum magnetron sputter deposited amorphous SiO[sub 2] thin films.

Author

Li, B. Q., Kojima, I., and Zuo, J. M.

Subjects
*AMORPHOUS semiconductors, *THIN films, *MAGNETRONS
Abstract

The surface morphology evolution of amorphous SiO[sub 2] thin films deposited by ultrahigh vacuum radio-frequency magnetron sputtering was studied by atomic force microscopy. The results show that: (1) the surface roughness of the deposited films reduces with increased substrate temperatures; (2) the surface roughness increases with higher deposition pressures; and (3) there is a roughening transition at the critical thickness of ∼ 90 nm for the substrate temperature of 713 K. The results also show that the surface roughness at the early stages of growth evolves according to a power law. Further growth beyond the critical thickness leads to a sharp increase in roughness. The experimental results are compared with the previous theoretical and experimental studies on surface evolution during sputter deposition, and discussed in terms of the competition between surface diffusion and shadowing. [ABSTRACT FROM AUTHOR]

Published
2002
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27. Changes in the electronic structure of CuInS2 thin films by Na incorporation

Author

Kyushu Inst Technol, Fac Engn, Dept Mat Sci, Natl Inst Res Inorgan Mat, Asahi Chem Ind Co Ltd, Natl Inst Mat & Chem Res, Fukuzaki, K, Kohiki, S, Yoshikawa, H, Fukushima, S, Watanabe, T, Kojima, I, Kyushu Inst Technol, Fac Engn, Dept Mat Sci, Natl Inst Res Inorgan Mat, Asahi Chem Ind Co Ltd, Natl Inst Mat & Chem Res, Fukuzaki, K, Kohiki, S, Yoshikawa, H, Fukushima, S, Watanabe, T, and Kojima, I

Abstract

type:Journal Article, For Na-free and Cu-deficient CuInS2 thin films with chalcopyrite structure, electron spectra of core levels and valence band were similar to each other in spite of a difference in Cu deficiency. Incorporation of Na with the CuInS2 films caused peak shifts by -0.5 eV for the core levels without changes in both linewidth and shape. The electron density of states, deeper by 1-5 eV than that from Cu d-S p hybridization centered at around 2.5 eV, increased by the Na incorporation, and increments in the electron density of states, were larger for the films with larger the Cu deficiency. The Na incorporation yielded a surface layer expressed as (Na,Cu)InS2 on the Cu deficient CuInS2 films. (C) 1998 American Institute of Physics., source:http://www.aip.org, source:https://doi.org/10.1063/1.122168

Published
2017

29. Nanoscale structural change in a sputter-deposited SiL2/a-Si/SiO2 sandwich

Author

Li, B. Q., Xu, W. T., Fujimoto, T., and Kojima, I.

Subjects
High resolution spectroscopy -- Usage, Sputtering (Physics) -- Research, Silicon compounds -- Research, Silicon compounds -- Electric properties, Physics
Abstract

Research is done on direct evidence that annealing a sputter-deposited SiO2/a-Si/SiO2 sandwiched structure on Si(100) results in the Si layer to expand. In conclusion, high-resolution electron microscopy examination further identified the formation of Si nanocrystals, the increase in thickness of the Si layer and the presence of oxygen-rich nanocavities at the Si/SiO2 interface, which confirms the XRR and ADP calculations.

Published
2004

30. Surface evolution of ultrahigh vacuum magnetron sputter deposited amorphous SiO2 thin films

Author

Li, b.Q., Kojima, I., and Zuo, J.M.

Subjects
Atomic force microscopy -- Research, Silicon -- Optical properties, Magnetrons -- Research, Dielectric films -- Optical properties, Thin films -- Optical properties, Physics
Abstract

The surface morphology evolution of amorphous SiO2 thin films deposited by ultrahigh vacuum radio frequency magnetron sputtering is studied by atomic force microscopy. The results show that the surface roughness of the deposited films reduced with increased substrate temperatures.

Published
2002

36. Nanoscale structural change in a sputter-deposited SiO[sub 2]/a-Si/SiO[sub 2] sandwich.

Author

Li, B. Q., Xu, W. T., Fujimoto, T. T., and Kojima, I.

Subjects
SPUTTERING (Physics), SILICON oxide, REFLECTANCE, NANOCRYSTALS, SURFACES (Technology), COLLISIONS (Nuclear physics), OPTICAL reflection, NANOPARTICLES
Abstract

We report direct evidence that annealing a sputter-deposited SiO[sub 2]/a-Si/SiO[sub 2] sandwiched structure on Si(100) results in the Si layer to expand. X-ray reflectivity (XRR) revealed the thickness of the Si layer to be temperature-dependent. Auger depth profiling (ADP) detected marked difference in the annealing behavior between the SiO[sub 2]/a-Si and a-Si/SiO[sub 2] interfaces and oxygen diffusion into the Si layer at the a-Si/SiO[sub 2] interface. High-resolution electron microscopy observation further identified the formation of Si nanocrystals, the increase in thickness of the Si layer, and the presence of oxygen-rich nanocavities at the Si/SiO[sub 2] interface, which confirms the XRR and ADP measurements. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Published
2004
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37. Diagnostic performance of MR imaging of three major salivary glands for Sjögren's syndrome.

Author

Kojima, I, Sakamoto, M, Iikubo, M, Kumamoto, H, Muroi, A, Sugawara, Y, Satoh ‐ Kuriwada, S, and Sasano, T

Subjects
*MAGNETIC resonance imaging evaluation, *RESEARCH methodology, *RESEARCH funding, *SALIVARY glands, *SJOGREN'S syndrome, *RETROSPECTIVE studies
Abstract

Objective We analyzed the diagnostic performance of the MR imaging findings of the parotid, submandibular, and sublingual glands to discriminate between patients with and without Sjögren's syndrome. Methods We retrospectively analyzed the correlation between the MR imaging and histopathological findings obtained from 69 patients with clinically suspected Sjögren's syndrome. We evaluated the heterogeneous signal intensity distribution on T1- and T2-weighted images, the multiple high-signal-intensity spots on MR sialograms, and the volume of the parotid, submandibular, and sublingual salivary glands. Results The multiple high-signal-intensity spots in the parotid gland showed the highest sensitivity and diagnostic accuracy (82% and 83%, respectively). In addition, the multiple high-signal-intensity spots and the heterogeneous signal intensity distribution in the submandibular gland showed high specificity (100% and 88%, respectively). The volume of the submandibular gland, but not that of the parotid or sublingual gland, was smaller in patients with Sjögren's syndrome. Conclusions The presence of multiple high-signal-intensity spots on an MR sialogram in the parotid gland should be considered the best diagnostic indicator for Sjögren's syndrome. The presence of spots, heterogeneity, and the change to smaller volumes in the submandibular gland were also helpful because of their high specificity, particularly in advanced cases. [ABSTRACT FROM AUTHOR]

Published
2017
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38. The rpoZ Gene, Encoding the RNA Polymerase Omega Subunit, Is Required for Antibiotic Production and Morphological Differentiation in Streptomyces kasugaensis

Author

Masayuki Kobayashi, Akira Arisawa, Satoshi Mizuno, Hisayoshi Akagawa, Fukasawa A, Kojima I, and Kano Kasuga

Subjects
Molecular Sequence Data, Mutant, Sigma Factor, Genetics and Molecular Biology, Kasugamycin, Microbiology, Streptomyces, Open Reading Frames, chemistry.chemical_compound, Plasmid, Bacterial Proteins, Sigma factor, Morphogenesis, Amino Acid Sequence, Cloning, Molecular, Gene, Molecular Biology, Aerial mycelium formation, Genetics, Base Sequence, biology, Morphological differentiation, fungi, Streptomyces coelicolor, DNA-Directed RNA Polymerases, Gene Expression Regulation, Bacterial, Sequence Analysis, DNA, Antibiotic production, biology.organism_classification, Molecular biology, Anti-Bacterial Agents, DNA-Binding Proteins, Complementation, Aminoglycosides, chemistry, RNA polymerase omega subunit, Mutation, Erratum, Sequence Alignment
Abstract

The occurrence of pleiotropic mutants that are defective in both antibiotic production and aerial mycelium formation is peculiar to streptomycetes. Pleiotropic mutant KSB was isolated from wild-type Streptomyces kasugaensis A1R6, which produces kasugamycin, an antifungal aminoglycoside antibiotic. A 9.3-kb DNA fragment was cloned from the chromosomal DNA of strain A1R6 by complementary restoration of kasugamycin production and aerial hypha formation to mutant KSB. Complementation experiments with deletion plasmids and subsequent DNA analysis indicated that orf5 , encoding 90 amino acids, was responsible for the restoration. A protein homology search revealed that orf5 was a homolog of rpoZ , the gene that is known to encode RNA polymerase subunit omega (ω), thus leading to the conclusion that orf5 was rpoZ in S. kasugaensis . The pleiotropy of mutant KSB was attributed to a 2-bp frameshift deletion in the rpoZ region of mutant KSB, which probably resulted in a truncated, incomplete ω of 47 amino acids. Furthermore, rpoZ -disrupted mutant R6D4 obtained from strain A1R6 by insertion of Tn 5 aphII into the middle of the rpoZ -coding region produced neither kasugamycin nor aerial mycelia, similar to mutant KSB. When rpoZ of S. kasugaensis and Streptomyces coelicolor , whose deduced products differed in the sixth amino acid residue, were introduced into mutant R6D4 via a plasmid, both transformants produced kasugamycin and aerial hyphae without significant differences. This study established that rpoZ is required for kasugamycin production and aerial mycelium formation in S. kasugaensis and responsible for pleiotropy.

Published
2003

39. Accessing RDF(S) data resources in service-based Grid infrastructures

Author

Esteban-Gutiérrez, M., Kojima, I., Pahlevi, S. M., Corcho, Oscar, Gómez-Pérez, A., Esteban-Gutiérrez, M., Kojima, I., Pahlevi, S. M., Corcho, Oscar, and Gómez-Pérez, A.

Abstract

We describe the results of the RDF(S) activity within the Open Grid Forum (http://www.ogf.org) (OGF) Database Access and Integration Services (DAIS) Working Group (http://forge.gridforum.org/projects/dais-wg) whose objective is to develop standard service-based grid access mechanisms for data expressed in RDF and RDF Schema. We produce two specifications, focused on the provision of SPARQL querying capabilities for accessing RDF data and a set of RDF Schema ontology handling primitives for creating, retrieving, updating, and deleting RDF data. In this paper we present a set of use cases that justify this work and an overview of these specifications, which will enter in editorial process at OGF25. We conclude by outlining the future work that will be made in the context of this standardization process.

Published
2009

40. Abstract P1-01-20: Clinicopathlogic Analysis of Invasive Breast Carcinoma with Micropapillary Component

Author

Yamanaka, T, primary, Suganuma, N, additional, Yamanaka, A, additional, Kojima, I, additional, Nishiyama, S, additional, Mukaibashi, T, additional, Nakayama, H, additional, Matsuura, H, additional, Matsuzu, K, additional, Chiba, A, additional, Inaba, M, additional, Rino, Y, additional, Yoshida, A, additional, Shimizu, S, additional, and Masuda, M, additional

Published
2012
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41. AKI - Experimental

Author

Kaynar, K., primary, Kaynar, K., additional, Ersoz, S., additional, Aliyazioglu, R., additional, Uzun, A., additional, Ulusoy, S., additional, Al, S., additional, Ozkan, G., additional, Cansiz, M., additional, Bertocchio, J.-P., additional, Lancon, J., additional, El Moghrabi, S., additional, Galmiche, G., additional, Duong Van Huyen, J.-P., additional, Rieu, P., additional, Jaisser, F., additional, Albertoni, G., additional, Andrade, S., additional, Barreto, J. A., additional, Borges, F., additional, Schor, N., additional, Ho, W.-Y., additional, Chen, S.-H., additional, Tseng, C.-J., additional, Bienholz, A., additional, Feldkamp, T., additional, Weinberg, J. M., additional, Suller Garcia, J., additional, Naves, M., additional, Aparecida Reis, L., additional, Simoes, M. d. J., additional, S Almeida, W., additional, Moreau Longo, V., additional, Segreto, H. R. C., additional, Ghoneim, A., additional, Elkholy, A., additional, Medhat Abbas, T., additional, El Hadeedy, M., additional, Elhusseini, F., additional, Elessawey, B., additional, Eltanaihy, E., additional, Lotfy, A., additional, Eldesoky, S., additional, Sheashaa, H., additional, Sobh, M., additional, Minning, D. M., additional, Warnock, D., additional, Mohamed, A. S., additional, Wirthlin, J. B., additional, Chintalacharuvu, S. R., additional, Boone, L., additional, Brenner, R. M., additional, Santina Christo, J., additional, Dos Santos Passos, C., additional, Rene de Alencar, D., additional, De Braganca, A. C., additional, Canale, D., additional, Goncalves, J. G., additional, Brandao, T. P. B., additional, Shimizu, M. H. M., additional, Volpini, R. A., additional, Seguro, A. C., additional, Andrade, L., additional, Lee, J.-W., additional, Kim, H. K., additional, Cho, W. Y., additional, Jo, S.-K., additional, Cho, E., additional, Hocherl, K., additional, Schmidt, C., additional, Mulay, S. R., additional, Kulkarni, O. P., additional, Rupanagudi, K. V., additional, Migliorini, A., additional, Liapis, H., additional, Anders, H.-J., additional, Pevzner, I., additional, Chupyrkina, A., additional, Plotnikov, E., additional, Zorov, D., additional, Lopez-Novoa, J.-M., additional, Eleno, N., additional, Perez-Barriocanal, F., additional, Arevalo, M., additional, Docherty, N., additional, Castellano, G., additional, Divella, C., additional, Loverre, A., additional, Stasi, A., additional, Curci, C., additional, Rossini, M., additional, Ditonno, P., additional, Battaglia, M., additional, Daha, M. R., additional, Van Kooten, C., additional, Gesualdo, L., additional, Schena, F. P., additional, Grandaliano, G., additional, Tsuda, H., additional, Kawada, N., additional, Iwatani, H., additional, Moriyama, T., additional, Takahara, S., additional, Rakugi, H., additional, Isaka, Y., additional, Schley, G., additional, Kalucka, J., additional, Klanke, B., additional, Jantsch, J., additional, Olbrich, S., additional, Baumgartl, J., additional, Amann, K., additional, Eckardt, K.-U., additional, Weidemann, A., additional, Dolgolikova, A., additional, Pilotovich, V., additional, Ivanchik, G., additional, Shved, I., additional, Banki, N. F., additional, Antal, Z., additional, Hosszu, A., additional, Koszegi, S., additional, Vannay, A., additional, Wagner, L., additional, Prokai, A., additional, Muller, V., additional, Szabo, A. J., additional, Fekete, A., additional, Farrag, S., additional, Abulasrar, S., additional, Salama, , M., additional, Amin, M., additional, Ali, A., additional, Rubera, I., additional, Duranton, C., additional, Cougnon, M., additional, Melis, N., additional, Tauc, M., additional, Jankauskas, S., additional, Morosanova, M., additional, Pulkina, N., additional, Zorova, L., additional, Shin, Y. T., additional, Kim, S. S., additional, Chang, Y. K., additional, Choi, D. E., additional, Na, K.-R., additional, Lee, K. W., additional, Choi, J.-Y., additional, Jin, D.-C., additional, Cha, J.-H., additional, Schneider, R., additional, Betz, B., additional, Meusel, M., additional, Held, C., additional, Wanner, C., additional, Gekle, M., additional, Sauvant, C., additional, Pisani, A., additional, Rossano, R., additional, Mancini, A., additional, Arfian, N., additional, Yagi, K., additional, Nakayama, K., additional, Ali, H., additional, Mayasari, D. S., additional, Purnomo, E., additional, Emoto, N., additional, Efrati, S., additional, Berman, S., additional, Abu Hamad, R., additional, Weissgarten, J., additional, Scherbaum, C. R., additional, Allam, R., additional, Lichtnekert, J., additional, Darisipudi, M. N., additional, Hagele, H., additional, Hohenstein, B., additional, Hugo, C., additional, Schaefer, L., additional, Corsi, C., additional, Ferramosca, E., additional, Grandi, E., additional, Pisoni, L., additional, Rivolta, I., additional, Dalpozzo, B., additional, Hoxha, E., additional, Severi, S., additional, Santoro, A., additional, Laurent, M., additional, Cedric, R., additional, Dominique, C., additional, Sophie, V., additional, Nochy, D., additional, Loic, G., additional, Patrice, C., additional, Chantal, J., additional, Marie-Christine, V., additional, Alexandre, H., additional, Eric, R., additional, Cantaluppi, V., additional, Medica, D., additional, Quercia, A. D., additional, Figliolini, F., additional, Dellepiane, S., additional, Randone, O., additional, Segoloni, G. P., additional, Camussi, G., additional, Ahn, B.-H., additional, Kim, S. H., additional, Yasue Saito Miyagi, M., additional, Camara, N., additional, Cerqueira Leite Seelaender, M., additional, Maceratesi Enjiu, L., additional, Estler Rocha Guilherme, P., additional, Pisciottano, M., additional, Hiyane, M., additional, Yuri Hayashida, C., additional, De Andrade Oliveira, V., additional, Olsen Saraiva Camara, N., additional, Tami Amano, M., additional, Sancho-Martinez, S. M., additional, Sanchez-Juanes, F., additional, Vicente, L., additional, Gonzalez-Buitrago, J. M., additional, Morales, A. I., additional, Lopez-Novoa, J. M., additional, Lopez-Hernandez, F. J., additional, Chen, J.-S., additional, Chang, L.-C., additional, Chen, C.-C., additional, Park, M. Y., additional, Choi, S. J., additional, Kim, J. G., additional, Hwang, S. D., additional, Vicente-Vicente, L., additional, Ferreira, L., additional, Prieto, M., additional, Garcia-Sanchez, O., additional, Sevilla, M. A., additional, Lopez-Novoa, F. J., additional, Christoph, K., additional, Kuper, C., additional, Maria-Luisa, F., additional, Franz-Xaver, B., additional, Neuhofer, W., additional, Vervaet, B., additional, Le Clef, N., additional, Verhulst, A., additional, D'haese, P., additional, Tanaka, T., additional, Yamaguchi, J., additional, Eto, N., additional, Kojima, I., additional, Fujita, T., additional, Nangaku, M., additional, Wystrychowski, A., additional, Wystrychowski, G., additional, Obuchowicz, E., additional, Grzeszczak, W., additional, Wiecek, A., additional, Esposito, C., additional, Torreggiani, M., additional, Castoldi, F., additional, Migotto, C., additional, Serpieri, N., additional, Grosjean, F., additional, Manini, A., additional, Pertile, E., additional, and Dal Canton, A., additional

Published
2012
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45. A unified nomenclature for the superfamily of TRP cation channels.

Author

Montell, C., Birnbaumer, L., Flockerzi, V., Bindels, R.J.M., Bruford, E.A., Caterina, M.J., Clapham, D.E., Harteneck, C., Heller, S., Julius, D., Kojima, I., Mori, Y., Penner, R., Prawitt, D., Scharenberg, A.M., Schultz, G., Shimizu, N., Zhu, M., Montell, C., Birnbaumer, L., Flockerzi, V., Bindels, R.J.M., Bruford, E.A., Caterina, M.J., Clapham, D.E., Harteneck, C., Heller, S., Julius, D., Kojima, I., Mori, Y., Penner, R., Prawitt, D., Scharenberg, A.M., Schultz, G., Shimizu, N., and Zhu, M.

Abstract

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Published
2002

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