Haruhisa Hayashi

We developed an AR molecular graphics application for chemical education at secondary level. Flash which can execute on all platforms is used as a programming language for software development for smartphone, which the possession rate of which in junior and senior high school students is high. By developing and mounting the AR function, students can examine molecular graphics in 3D or when they look at a marker printed in a text or a handout just to read. To develop the web interface for making molecular data, the teacher can use molecular graphics in 3D easily when necessary.

In April 2013, the University of Hyogo was transformed into the municipal university corporation. Therefore, the business-use systems for financial, traveling-expenses, personal affairs and salary, which was using the prefectual system by exclusive-use PCs, s introduced newly. Furthermore, the cost of such a change would be considerable, we have discussed the burden sharing with the Hyogo prefecture. In this paper, we explain the design and introduction of new systems.

兵庫県立大学では，教育および研究のインフラとなる情報システム (ネットワークシステム・情報処理教育システム・遠隔授業システム・学生情報システム・図書システム) のリプレイスをおこない，2009 年 3 月から運用を開始した．これら新システムの構築と移行などに関して報告する．We planned to replace some information systems (such as network system, information processing education system, distance learning system, student information system and library information system) as infrastructure of academic activities for the University of Hyogo, and have started these operation at March 2009. In this paper, we report our construction and switchover to new systems.

2004 年 4 月に県立大学が統合し発足した兵庫県立大学は，6 つのキャンパスや研究所などが広く県内に点在している．これに伴い，独自 DV 方式により各キャンパスを結ぶ双方向配信可能な遠隔授業システムを導入した．本稿ではこの遠隔授業システムの運用評価と，新システム導入に向けた課題点・改善点などを報告する．The University of Hyogo was inaugurated by integrating prefectural universities in April 2004 would consist of six campuses and some laboratories, scattered across Hyogo Prefecture. Therefore, we introduced the Distance Learning System using digital video over IP, with interactive communications between each campus. We report our evaluation of this system and improvement in the next system.

Firefly luciferase is a well-known enzyme that participates in the bioluminescence reaction. Recently, it was reported that this enzyme also exhibits enantioselective thioester formation activity of 2-arylpropanoic acid such as ketoprofen. However, the enantiodifferential mechanism was still unknown. Therefore to clarify the reason of enantioselective thioester formation toward ketoprofen, we have performed molecular dynamics (MD) simulations for three kinds of firefly luciferase / acyl-AMP intermediate analogue complexes. Targeted substrates were N-acylsulfamate derivatives of R-ketoprofen, S-ketoprofen and 3-benzoylphenylacetic acids. Our results show that the dynamic behavior of Ser200 and Ser201 around the asymmetric carbon atom in the complexes is quite different.

We describe a new strategy for multipyrene modification of RNA sequences to form unique structures of pyrene aromatic arrays, the "pyrene-zipper array", on duplex RNA that exhibits remarkably strong excimer fluorescence.

In controlling spam mails, it is important not only to reduce spam mails, but also to deliver non-spam mails. It is also important to lower the cost in small and medium enterprises. The anti-spam method using greylisting only after working hours and throttling was implemented at Technology Research Institute of Osaka Prefecture. And we tried to reduce spam mails without maintenance of white list and database. In this paper, we describe the usefullness of this method from questionnaire survey and mail log analysis. After that, we report the result that we tried to reduce spam mails in the university laboratory with this method.

It is known that RNA modified with the pyrenyl group (pyren-RNA) which uses the pyrene moiety as a fluorescent chromophore shows a remarkable increase in fluorescence when the double helix is formed with the complementary strand RNA, compared to the single strand pyrene-RNA, and that this phenomenon is not seen with DNA. For the purpose of designing a sequence recognition probe based on these phenomena, detailed data of the pyrenyl moiety in the pyrene-RNA and pyrene-DNA of double stranded structures are observed with MD simulation. In addition, the influence of mismatched combination of base in the complementary strand was examined. As a result, it was revealed that in the full-match double stranded pyrene-DNA the pyrene moiety stays inside the helix but in the full-match double stranded pyrene-RNA pyrene was thrusted out of the helix. Mismatch sequence in the pyrene-RNAdouble strand influenced the behavior of the pyrenyl moiety when the mismatch position was located close to the pyrene modified position.

By using the public/commercial wide-area and broadband network (EoMPLS and ATM-MPLS etc) as the campus intranet, it seems as though the scattered campuses are in the same Local Area Network. We constructed the computer network system using such a network, to receive the same service for all users in each campus. In the educational institution, the utilization of such network service is expected to apply the distance learning with high quality video and sound. Therefore we show two cases of the system implementation and operation using the wide-area and broadband network with the educational institution.

We performed X-ray crystallographic analyses of 6-aminohexanoate-dimer hydrolase (Hyb-24DN), an enzyme responsible for the degradation of nylon-6, an industry by-product, and of a complex between Hyb-24DN-A(112) (S112A-mutant of Hyb-24DN) and 6-aminohexanoate-linear dimer (Ald) at 1.58 A and 1.4 A resolution, respectively. In Hyb-24DN, Asp181-O(delta) forms hydrogen bonds with Tyr170-O(eta), -two of the catalytic and binding amino acids, and a loop between Asn167 and Val177. This state is the so-called open form, allowing its substrate to bind in the space between the loop and catalytic residues. Upon substrate binding (in Hyb-24DN-A(112)/Ald complex), the loop is shifted 4.3 A at Tyr170-C(alpha), and the side-chain of Tyr170 is rotated. By the combined effect, Tyr170-O(eta) moves a total of 10.5 A, resulting in the formation of hydrogen bonds with the nitrogen of amide linkage in Ald (closed form). In addition, electrostatic interaction between Asp181-O(delta) and the amino group in Ald stabilizes the substrate binding. We propose here that the enzyme catalysis proceeds according to the following steps: (i) Ald-induced transition from open to closed form, (ii) nucleophilic attack of Ser112 to Ald and formation of a tetrahedral intermediate, (iii) formation of acyl enzyme and transition to open form, (iv) deacylation. Amino acid substitutions reducing the enzyme/Ald interaction at positions 181 or 170 drastically decreased the Ald-hydrolytic activity, but had very little effect on esterolytic activity, suggesting that esterolytic reaction proceeds regardless of conversion. Present models illustrate why new activity against the nylon oligomer has evolved in an esterase with beta-lactamase folds, while retaining the original esterolytic functions.

RNA oligomers having multiple (2 to 4) pyrenylmethyl substituents at the 2'-O-sugar residues were synthesized. UV-melting studies showed that the pyrene-modified RNAs could form duplexes with complementary RNA sequences without loss of thermal stability. Absorption, fluorescence, and circular dichroism (CD) spectra revealed that the incorporated pyrenes projected toward the outside of A-form RNA duplexes and assembled in helical aromatic arrays along the minor grooves of the RNA duplexes. Results of computer simulations agreed with the assembled structures of the pyrenes. The helical pyrene arrays exhibited remarkably strong excimer fluorescence, which was dependent on the sequence contexts of RNA duplexes.

Greylisting is known as one of the highest effective method within anti-seam method. However, it has issues that requires the maintenance of the list, and forces delivery delay of e-mails. So, we tried to resolve those issues by transfering e-mails without retransmission request during working hours. And also we used throttling to try to reduce spam mails during working hours. In this paper, we report on the controlling spa mails with greylisting and throttling, and it's effectiveness.

The University of Hyogo was inaugurated by integrating three prefectural universities in April 2004. Using the 'Hyogo Information Highway' network as the campus intranet, we constructed the Student Information System, the Library System, the Computer System for Education, and the Distance Learning System (DV and H.323). In this paper, we report our reconstruction, implementation and operation of those systems.

"Modrast-P", which we have developed, has distinctive functions for displaying molecular models, especially, the capacity to display models clipped by single or double plane(s). This function is useful to show inner structures of inclusion complexes or active sites of bio-molecules, which are otherwise hidden by outer parts of molecules. However, Modrast-P was dependent on hardware and OS, so we improved this program using GTK+, which was one of the toolkits of the X Window System, and named it "Modrast-P with GTK+". For the clipping function, the operations to specify the clipping plane are facilitated with GUI (graphical user interface). In addition, some useful functions such as animation and numerical analysis for results of Molecular Dynamics (MD) simulation with AMBER have been implemented.

Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene-DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene-RNA/RNA and the pyrene-DNA/DNA duplexes.

AMBER (Assisted Model Building with Energy Refinement) is a powerful tool for simulations of bio-molecules and so on. To simulate DNA molecules with new residues that are not registered in the AMBER database, it is necessary to register them on this database by using one of the AMBER modules, PREP. However, the format of the PREP input file is very complicated, and it is hard to make by hand. Therefore, in this work, in order to make the PREP input file interactively with visualization, we add a function to our molecular structural display system, "Modrast-P". By using this function, the PREP input file can be made easily and efficiently.

A support program for AMBER was developed on the basis of the biomolecular graphics program “Modrast-P". This program has three features, which are : 1) Setting up of input files for AMBER. It is easy and efficient to make input files for AMBER modules (Figure 1) by using interactive and graphical operations. 2) Molecular modeling for building the initial structure of the molecule for molecular dynamics calculation by use of the extended function of Modrast-P. 3) Animations of atomic trajectory files from molecular dynamics simulations, calculations of atom-to-atom distances and the extraction of potential energies from output files in order to draw graphs for getting quantitative information, are possible.As an example use of this program, the structure of DNA containing anthraquinone groups was simulated (Figures 2,3).This program runs on any UNIX workstations and personal computers where PC-UNIX, such as Linux, are installed.

The synthesis of 2'-(6-dimethylamino-2-naphthamide)uridine [U(DAN)] has been described. The nucleoside was converted to the 5'-dimethoxylrityl nucleoside phosphoramidite which could be used for incorporation of U(DAN) into the desired positions of the oligonucleotide sequence. (C) 1997 Elsevier Science Ltd.

The oligonucleotides containing 2'-(6-dimethylamino-2-naphthamide)uridine [U(DAN)] at the different position were synthesized by the fully automated solid phase phosphoramidite methods. The UV melting profiles for the U(DAN)-modified oligonucleotides with complementary DNA exhibited sigmoidal curves whose shapes were similar to those for the unmodified duplexes.

Molecular dynamics simulations have been performed for liquid n-butane and ethylene glycol (1,2-ethanediol; EG) in order to understand liquid structures in terms of both inter- and intra-molecular interactions. Each n-butane molecule consists of four sites interacting with LJ potential, and with only one dihedral angle potential, while each EG molecule has six sites interacting through LJ and coulomb potentials together with three dihedral angle potentials. The flexible molecule has the tendency to be folded more intensely in the liquid state than that in the gas phase. Comparing aqueous solution of EG with Xe solution and gaseous state of EG, it is found that EG molecules more strongly favor the folded form by intramolecular interactions, especially by intramolecular hydrogen bond. © 1995.

Molecular dynamics simulations have been performed for ethylene glycol (ethane-1,2-diol, EG) in water. Each EG molecule consists of six sites interacting through Lennard-Jones and coulomb potentials together with three dihedral angle potentials. A comparison of the behaviour of EG molecules in water and in Xe shows that in the latter solvent the EG molecules tend to fold, unlike those in water. In order to investigate how the intramolecular interaction affects the intermolecular hydrogen bonds, some rigid-EG models are also examined.

We have performed molecular dynamics simulations for liquid n-butane in order to understand liquid structures in terms of both inter- and intra-molecular interactions. Each n-butane molecule consists of four sites interacting with LJ potential and only a dihedral angle is taken into account as the internal degree of freedom. The population of gauche conformations with respect to the ideal gas state is found to increase in the liquid state. To investigate how the intermolecular interaction affects the dihedral angle distribution, we also adopt the repulsive LJ potential (RLJ) model. It is found that the nearest neighbor packing of the methyl and/or methylene groups can be approximately represented by using only the repulsive interaction. From the dihedral angle distribution, however, the rate of the shift of RLJ model to gauche is larger than that of LJ model and the attractive force also plays a significant role in the conformational equilibrium. © 1993, Taylor & Francis Group, LLC. All rights reserved.