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Presence/Absence of Two Types of Z-DNA Binding Domains in the Genomes of Organisms from Archaea, Bacteria, and Eukaryotes and Its Implications

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Journal of Biomedical Science and Engineering 2019年第1期12卷 1-9页

作者： hiroshi nakashima Department of Clinical Laboratory Science Graduate Course of Medical Science and Technology School of Health Sciences Kanazawa University Kanazawa Japan

We conducted genome sequence analysis to examine the presence/absence of two types of Z-DNA binding domains in various organisms. We examined 68 organisms from archaea, 914 organisms from bacteria, and 199 organisms from eukaryotes. RecA protein from Escherichia coli has a Z-DNA binding domain and this protein promotes homologous recombination. All the organisms examined had this domain. This result indicated that this domain is essential for all the organisms. RNA editing enzyme, adenosine deaminase from human has another type of Z-DNA binding domain. This domain was observed in some organisms of archaea, bacteria, and eukaryotes. The presence/absence of Z-DNA binding domain in adenosine deaminase indicated that gain and loss of this domain had occurred in the process of evolution. The implication of presence and absence of this domain is discussed in this study.

关键词： Z-DNA Binding Domain recA Protein Adenosine Deaminase Acting on RNA Genome Sequence Analysis

Self-Assembled Conjugated Polymer Nanometer Scale Devices

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复旦学报（自然科学版） 2005年第5期44卷 709-710页

作者： Wenping Hu hiroshi nakashima Keiichi Torimitsu Yunqi Liu Daoben Zhu Laboratory of Organic Solids Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China NTT Basic Research Laboratories NTT Corporation 3-1 Morinosato Wakamiya Atsugi Kanagawa 243-0198 Japan

Nanometer scale devices, as the next generation devices of electronics, have got a worldwide attention and rapid development recently. Simultaneously, conjugated polymers have been applied in organic electronics successfully because of their outstanding electronic-photonic properties. However, as far as we know few reports have dealt with the fabrication of nanometer scale devices by using conjugated polymers, although the combination of nanometer scale devices and polymers will not only extend conjugated polymers to Nanoelectronics, but also excavate the behaviors of polymer molecules at nano-molecular level, such as the electron transport through polymer molecules. One reason for this case is due to the lack of rigidity for most *** results in the failure to bridge them between electrodes or to stand on substrates, therefore, fails to be characterized by scanning probe microscopy. Another reason is that the non-functionalized end-group of most polymers is impossible to graft on substrates through chemical bonds. Here, we introduce a self-assembled conjugated polymer can be used to fabricate nanodevices by self-assembly. The conjugated polymer is a derivative of poly(p-phenyleneethynylene)s (PPE) with thioacetyl end groups (Fig. 1). In general, it is known that for self-assembling ideal nanojunctions the materials should possess: a) conductivity, b) rigidity (for wiring and bridging between electrodes), and c) connectivity (for covalent attachment to metallic or semiconductor solid surfaces). PPE provides good conductivity owing to its special π-conjugated configuration. It is also believed that in principle PPE molecules possess rigidity because of the presence of the triple bond in their molecules,which prevents the rotation of adjacent phenyl rings with respect to each other.

关键词：自组合反应共轭聚合体纳米装置有机物电化学

Decreasing trend in prostate cancer with high serum prostate-specific antigen levels detected at first prostate-specific antigen-based population screening in Japan

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Asian Journal of Andrology 2014年第6期16卷 833-837页

作者： Yasuhide Kitagawa Kazuaki Machioka hiroshi Yaegashi Kazufumi nakashima Mitsuo Ofud Kouji Izumi Satoru Ueno Yoshifumi Kadono Hiroyuki Konaka Atsushi Mizokami Mikio Namiki Department of Integrative Cancer Therapy and Urology Kanazawa University Graduate School of Medical Science Kanazawa 920-8640 Japan

To clarify the recent trends in prostate-specific antigen （PSA） distribution in men in Japan, we analyzed the PSA distributions of men undergoing PSA-based population screening. We summarized the annual individual data of PSA-based population screening in Kanazawa, Japan, from 2000 to 2011, and analyzed baseline serum PSA values of the participants at the first population screening. Serum PSA distributions were estimated in all participants and those excluding prostate cancer patients according to age. From 2000 to 2011, 19 620 men participated aged 54-69 years old in this screening program. Mean baseline serum PSA level of all participants at the first screening was 2.64 ng m1-1 in 2000, and gradually decreased to approximately 1.30 ng ml-I in 2006. That of participants excluding prostate cancer patients was 1.46 ng m1-1 in 2000, and there was no remarkable change during the study period. The 95t＂ percentiles in the participants excluding prostate cancer patients detected at the first population screening of men aged 54-59, 60-64, and 65-69 years old were 2.90, 3.60, and 4.50 ng m1-1, respectively. After the commencement of population screening, the proportion of prostate cancer patients with high serum PSA levels decreased. However, there were no changes in serum PSA levels in men without prostate cancer. Age-specific PSA reference level of men without prostate cancer in Japan was similar to that in China and Korea.

关键词： age-specific prostate-specific antigen reference range prostate cancer prostate-specific antigen-based population screening serum prostate-specific antigen distribution

Hydrogen bonds are related to the thermal stability of 16S rRNA

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Journal of Biomedical Science and Engineering 2013年第1期6卷 19-24页

作者： hiroshi nakashima Ai Fukuoka Yuka Saitou Department of Clinical Laboratory Science Graduate Course of Medical Science and Technology School of Health Sciences Kanazawa University Kanazawa Japan

The number of base pairs in the 16S rRNA secondary structures of 51 bacterial sequences was counted, and the number of hydrogen bonds was estimated. The number of hydrogen bonds was highly correlated with the optimal growth temperature (OGT) rather than with the G + C content. Paired and unpaired nucleotides in mesophiles were compared to those in thermophiles. OGT exhibited a relationship with paired nucleotides but not with unpaired nucleotides. The total number of paired as well as unpaired nucleotides in mesophiles was very similar to that in thermophiles. However, the components in base pairs in mesophiles significantly differed from those in thermophiles. As compared with mesophiles, the number of G·C base pairs in thermophiles was high whereas that of A·U base pairs was low. In this study, we showed that hydrogen bonds are important for stabilizing 16S rRNAs at high temperatures.

关键词： Optimal Growth Temperature 16S Ribosomal RNA G + C Content Hydrogen Bonds Base Pairs Nucleotide Compositions

Differences in Amino Acid Composition between <i>α</i>and <i>β</i>Structural Classes of Proteins

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Journal of Biomedical Science and Engineering 2014年第11期7卷 890-918页

作者： hiroshi nakashima Yuka Saitou Nachi Usuki Department of Clinical Laboratory Science Graduate Course of Medical Science and Technology School of Health Sciences Kanazawa University Kanazawa Japan

The amino acid composition of α and β structural class of proteins from five species, Escherichia coli, Thermotoga maritima, Thermus thermophilus, yeast, and humans were investigated. Amino acid residues of proteins were classified into interior or surface residues based on the relative accessible surface area. The hydrophobic Leu, Ala, Val, and Ile residues were rich in interior residues, and hydrophilic Glu, Lys, Asp, and Arg were rich in surface residues both in α and β proteins. The amino acid composition of α proteins was different from that of β proteins in five species, and the difference was derived from the different contents of their interior residues between α and β proteins. α-helix content of α proteins was rich in interior residues than surface ones. Similarly, β-sheet content of β proteins was rich in interior residues than surface ones. The content of Leu residues was very high, approximately 20%, in interior residues of α proteins. This result suggested that the Leu residue plays an important role in the folding of α proteins.

关键词： Amino Acid Composition α and β Proteins Interior/Surface Residue Protein Domains Species-Specific Amino Acid Composition

Favorable and unfavorable amino acid residues in water-soluble and transmembrane proteins

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Journal of Biomedical Science and Engineering 2013年第1期6卷 36-44页

作者： hiroshi nakashima Ayano Yoshihara Kei-ichiro Kitamura Department of Clinical Laboratory Science Graduate Course of Medical Science and Technology School of Health Science Kanazawa University Kanazawa Japan

We analyzed the amino acid residues present in the water-soluble and transmembrane proteins of 6 thermophilic and 6 mesophilic species of the domains Archaea and Eubacteria, and characterized them as favorable or unfavorable. The characterization was performed by comparing the observed number of each amino acid residue to the expected number calculated from the percentage of nucleotides present in each gene. Amino acids that were more or less abundant than expected were considered as favorable or unfavorable, respectively. Comparisons of amino acid compositions indicated that the water-soluble proteins were rich in charged residues such as Glu, Asp, Lys, and His, whereas hydrophobic residues such as Trp, Phe, and Leu were abundant in transmembrane proteins. Interestingly, our results found that although the Trp residue was abundant in transmembrane proteins, it was not defined as favorable by our calculations, indicating that increased numbers of a particular amino acid does not necessary indicate it is a favorable residue. Amino acids with high G + C content such as Ala, Gly, and Pro were frequently observed as favorable in species with low G + C content. Comparatively, amino acids with low G + C content such as Phe, Tyr, Lys, Ile, and Met were frequently observed as favorable in species with high G + C content. These are the examples to increase the supply of amino acids than expected. Amino acids with neutral G + C content, i.e., Glu and Asp were favorable in water-soluble proteins from all species analyzed, and Cys was unfavorable both in water-soluble and transmembrane proteins. These results indicate that amino acid compositions are essentially determined by the nucleotide sequence of the genes, and the amino acid content is altered by a deviation from expectation.

关键词： Amino Acid Composition Nucleotide Composition Favorable and Unfavorable Residues Water-Soluble and Transmembrane Proteins Thermophilic and Mesophilic Species

Phototransistors of a Rigid Rod Conjugated Polymer

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Phototransistors of a Rigid Rod Conjugated Polymer

Photoluminescence Evaluation of Defects Generated during Temperature Ramp-up Process of SiGe-On-Insulator Virtual Substrate Fabrication

全国第八届有机固体电子过程暨华人有机光电功能材料学术讨论会

作者： nakashima hiroshi Torimitsu Keiichi NTT Basic Research Laboratories NTT Corporation3-1 Morinosato WakamiyaAtsugiKanagawaJapan 243-0198

Poly(para-phenylene ethynylene)s(PPEs),an important class of conjugated polymer materials,exhibit not only unique chemical and physical properties but also ideal rigidity,which makes them attractive for solid state optoelectronic ***,up to date,there rarely little reports have addressed their applications in organic field-effect transistors,not to mention the phototransistors,which not only realize the combination of light

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Photoluminescence Evaluation of Defects Generated during Tem...

黑龙江省中部地区大豆主栽品种有效株行距解析

2006 8th International Conference on Solid-State and Integrated Circuit Technology

作者： Dong Wang Seiichiro Ii Ken-ichi Ikeda Hideharu nakashima hiroshi nakashima Art Science and Technology Center for Cooperative ResearchKyushu University6-1 Kasuga-koenKasugaFukuoka 816-8580Japan Department of Molecular and Materials Sciences Interdisciplinary Graduate School of Engineering SciencesKyushu University6-1 Kasuga-koenKasugaFukuoka 816-8580Japan

ISBN: (纸本)1424401607

＜正＞Defects generated during the temperature ramping process were evaluated by photoluminescence（PL） for Si/SiGe/Si-on-insulater structure,which is the typical structure for SiGe-on-insulator（SGOI） virtual substrate fabrication using the Ge condensation by dry oxidation. The free exciton peaks were clearly observed for the as grown wafers and decreased with the increase of annealing ***-related PL signals at around 0.82,0.88,0.95 and 1.0 eV were observed and they also varied according to the annealing temperature and SiGe *** defect-related PL signals were also correlated to dislocation-related defects by transmission electron microscopy（TEM）.

关键词： Silicon germanium Transmission electron microscopy annealing ramp-up PNLIP gene CSH1 gene pickling line Virtual photoluminescence SiGe on insulator Substrates fabrication

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大豆科学 2007年第3期26卷 327-331页

作者：韩秉进金剑中嶋博中国科学院东北地理与农业生态研究所黑土生态重点实验室哈尔滨150081 日本北海道大学北方生物圏フィ■ルド科学.センタ■

运用作物有效营养面积理论,对大豆主产区黑龙江省中部垄作主栽大豆品种的有效株行距进行了试验研究与理论解析.研究表明黑龙江省中部地区的大豆有效株行距为47.0～63.0 cm.据此阐明目前生产上广泛采用67～70 cm的垄作,已超过了大豆的有... 详细信息

运用作物有效营养面积理论,对大豆主产区黑龙江省中部垄作主栽大豆品种的有效株行距进行了试验研究与理论解析.研究表明黑龙江省中部地区的大豆有效株行距为47.0～63.0 cm.据此阐明目前生产上广泛采用67～70 cm的垄作,已超过了大豆的有效株行距,造成了土壤资源的浪费.采用55 cm左右的垄距种植大豆,将会更有利于大豆群体产量的提高.该理论为目前黑龙江省北部地区栽培面积逐渐增大的大豆窄行垄栽培提供了有力的理论根据.

关键词：有效株行距大豆品种单株产量