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Search Results: 1 - 10 of 209 matches for " Sakae Arimoto "
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Properties of Hemolysin and Protease Produced by Aeromonas trota
Eizo Takahashi, Haruka Ozaki, Yoshio Fujii, Hidetomo Kobayashi, Hiroyasu Yamanaka, Sakae Arimoto, Tomoe Negishi, Keinosuke Okamoto
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0091149
Abstract: We examined the properties of exotoxins produced by Aeromonas trota (A. enteropelogenes), one of the diarrheagenic species of Aeromonadaceae. Nine of 19 A. trota isolates that grew on solid media containing erythrocytes showed hemolytic activity. However, the hemolytic activities of the culture supernatants of these hemolytic strains of A. trota were markedly lower than those of A. sobria when cultured in liquid medium, and the amount of hemolysin detected by immunoblotting using antiserum against the hemolysin produced by A. sobria was also low. A mouse intestine loop assay using living bacterial cells showed that A. trota 701 caused the significant accumulation of fluid, and antiserum against the hemolysin produced suppressed the enterotoxic action of A. trota 701. These results indicated that A. trota 701 was diarrheagenic and the hemolysin produced was the causative agent of the enterotoxic activity of A. trota. The hemolysin in A. sobria was previously shown to be secreted in a preform (inactive form) and be activated when the carboxy-terminal domain was cleaved off by proteases in the culture supernatant. Since mature hemolysin was detected in the culture supernatants of A. trota, we analyzed the extracellular protease produced by A. trota. Fifteen of 19 A. trota isolates that grew on solid media containing skim milk showed proteolytic activity. We subsequently found that most A. trota isolates possessed the serine protease gene, but not the metalloprotease gene. Therefore, we determined the nucleotide sequence of the serine protease gene and its chaperone A. trota gene. The results obtained revealed that the deduced amino acid sequences of serine protease and the chaperone were homologous to those of A. sobria with identities of 83.0% and 75.8%, respectively.
Regulation of bone destruction in rheumatoid arthritis through RANKL-RANK pathways
Sakae Tanaka
World Journal of Orthopedics , 2013, DOI: 10.5312/wjo.v4.i1.1
Abstract: Recent studies have demonstrated that osteoclasts, the primary cells responsible for bone resorption, are mainly involved in bone and joint destruction in rheumatoid arthritis (RA) patients. Recent progress in bone cell biology has revealed the molecular mechanism of osteoclast differentiation and bone resorption by mature osteoclasts. We highlight here the potential role of the receptor activator of nuclear factor κB ligand (RANKL)-RANK pathways in bone destruction in RA and review recent clinical trials treating RA by targeting RANKL.
Coloring ordinals by reals
Sakae Fuchino
Mathematics , 1997,
Abstract: We introduce several new set-theoretic axioms formulated in terms of coloring of ordinals by reals. We show that these axioms generalize the axioms considered by I.Juhasz, L.Soukup and Z.Szentmiklossy, and give a class of p.o.s including Cohen p.o.-sets which force the axioms. In appearance these axioms are somewhat similar to OCA but it appears that they are inconsistent with OCA.
A Simple Proof of the Classification of Normal Toeplitz Matrices
Akio Arimoto
Mathematics , 2002,
Abstract: We give an easy proof to show that every complex normal Toeplitz matrix is classified as either of type I or of type II. Instead of difference equations on elements in the matrix used in past studies, polynomial equations with coefficients of elements are used. In a similar fashion, we show that a real normal Toeplitz matrix must be one of four types: symmetric, skew-symmetric, circulant, or skew-circulant. Here we use trigonometric polynomials in the complex case and algebraic polynomials in the real case.
PCR-Mediated Detection of Endophytic and Phytopathogenic Fungi from Needles of the Japanese Black Pine, Pinus thunbergii  [PDF]
Junichi Kihara, Makoto Ueno, Sakae Arase
Open Journal of Forestry (OJF) , 2015, DOI: 10.4236/ojf.2015.54037
Abstract: A specific and sensitive polymerase chain reaction (PCR) assay based on the internal transcribed spacer (ITS) region of rDNA sequences was developed to detect endophytic and phytopathogenic fungi from needles of the Japanese black pine, Pinus thunbergii. Sequences of the ITS regions of Lophodermium conigenum, Lecanosticta acicola, Pestalotiopsis neglecta, Rhizosphaera kalkhoffii, and Septorioides pini-thunbergii were compared, and each specific primer pair for these species was designed. First, the designed primer pairs were tested for their specificity to detect each species. A PCR product was amplified only each combination of species and its specific primer pair, confirming the specificity of the designed primer pairs. These primer pairs were also tested on DNA extracted from the needles of P. thunbergii. The PCR products were amplified not only in needles with lesions but also in healthy needles without symptoms. Furthermore, several endophytic and phytopathogenic fungi could be simultaneously detected from the same region in a needle. The PCR-mediated detection method developed in this study will be a valuable tool for the detection of the endophytic and phytopathogenic fungi, not only as a rapid diagnostic tool for early detection but also for monitoring variations in both the quality and quantity of the endophytic and phytopathogenic fungi in needles in Japanese black pines.
Secondary-Structure Design of Proteins by a Backbone Torsion Energy
Yoshitake Sakae,Yuko Okamoto
Physics , 2005, DOI: 10.1143/JPSJ.75.054802
Abstract: We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles phi and psi. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both phi and psi can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the alpha-helix-forming-tendencies by lowering/raising the torsion-energy surface in the alpha-helix region and likewise increase/decrease the beta-sheet-forming tendencies by lowering/raising the surface in the beta-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming-tendencies by performing folding simulations of alpha-helical and beta-hairpin peptides.
Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability
Yoshitake Sakae,Yuko Okamoto
Physics , 2013,
Abstract: We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $\psi$ (N-C$^{\alpha}$-C-N) and $\zeta$ (C$^{\beta}$-C$^{\alpha}$-C-N) of the backbone dihedral angles. We then performed folding simulations of $\alpha$-helical and $\beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.
More Set-theory around the weak Freese-Nation property
Sakae Fuchino,Lajos Soukup
Mathematics , 1996,
Abstract: In this paper, we introduce a very weak square principle which is even weaker than the similar principle introduced by Foreman and Magidor. A characterization of this principle is given in term of sequences of elementary submodels of H(\chi). This is used in turn to prove a characterization of kappa-Freese-Nation property under the very weak square principle and a weak variant of the Singular Cardinals Hypothesis. A typical application of this characterization shows that under 2^{\aleph_0}<\aleph_\omega and our very weak square for \aleph_\omega, the partial ordering [omega_\omega]^{<\omega} (ordered by inclusion) has the aleph_1-Freese-Nation property. On the other hand we show that, under Chang's Conjecture for \aleph_\omega the partial ordering above does not have the aleph_1-Freese-Nation property. Hence we obtain the independence of our characterization of the kappa-Freese-Nation property and also of the very weak square principle from ZFC.
Remarks on a paper by Juhász and Kunen
Sakae Fuchino,Stefan Geschke
Mathematics , 2003,
Abstract: We give an equivalent, but simpler formulation of the axiom SEP introduced by Juhasz and Kunen. Our formulation shows that many of the consequences of the weak Freese-Nation Property of $\mathcal P(\omega)$ already follow from SEP. We show that it is consistent that SEP holds while $\mathcal P(\omega)$ fails to have the $(\aleph_1,\aleph_0)$-ideal property, which has been introduced by Hart and Dow . This answers a question addressed independently by Fuchino and by Kunen. We also consider some natural variants of SEP and show that certain changes in the definition of SEP do not lead to a different principle. This answers a question addressed by Blass.
Amino-acid-dependent main-chain torsion-energy terms for protein systems
Yoshitake Sakae,Yuko Okamoto
Quantitative Biology , 2012, DOI: 10.1063/1.4774159
Abstract: Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameters for $\psi$ and $\psi'$ angles for each amino acid by using our optimization method, which is one of the knowledge-based approach. In order to test the validity of the new force-field parameters, we then performed folding simulations of $\alpha$-helical and $\beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff03 force field.
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