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  1. Article ; Online: Significant variants of type 2 diabetes in the Arabian Region through an Integration of exome databases.

    Kosuke Goto / Katsuhiko Mineta / Satoru Miyazaki / Takashi Gojobori

    PLoS ONE, Vol 16, Iss 4, p e

    2021  Volume 0249226

    Abstract: Type 2 diabetes (T2D) is a major global health issue, and it has also become one of the major diseases in Arab countries. In addition to the exome databases that have already been established, whole exome sequencing data for the Greater Middle East are ... ...

    Abstract Type 2 diabetes (T2D) is a major global health issue, and it has also become one of the major diseases in Arab countries. In addition to the exome databases that have already been established, whole exome sequencing data for the Greater Middle East are now available. To elucidate the genetic features of T2D in the Arabian Peninsula, we integrated two exome databases (gnomAD exome and the Greater Middle East Variome Project) with clinical information from the ClinVar. After the integration, we obtained 18 single nucleotide polymorphisms and found two statistically and clinically significant variants in two genes, SLC30A8 rs13266634 and KCNJ11 rs5219. Interestingly, the two genes are linked to the uptake of the metals, Zn and K respectively, which indicating the regional features of the genetic variants. The frequency of the risk allele of rs13266634 among individuals in the Arabian Peninsula was higher than among individuals in other regions. On the other hand, the frequency of the risk allele of rs5219 in the Arabian Peninsula was lower than that in other regions. We identified and characterized T2D-related variants that show unique tendencies in the Arabian Peninsula. Our analyses contribute to and provide guidance for the clinical research of T2D in the Arabian Peninsula.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Direct Inhibition of SARS-CoV-2 Spike Protein by Peracetic Acid

    Yuichiro Yamamoto / Yoshio Nakano / Mana Murae / Yoshimi Shimizu / Shota Sakai / Motohiko Ogawa / Tomoharu Mizukami / Tetsuya Inoue / Taishi Onodera / Yoshimasa Takahashi / Takaji Wakita / Masayoshi Fukasawa / Satoru Miyazaki / Kohji Noguchi

    International Journal of Molecular Sciences, Vol 24, Iss 1, p

    2022  Volume 20

    Abstract: Peracetic acid (PAA) disinfectants are effective against a wide range of pathogenic microorganisms, including bacteria, fungi, and viruses. Several studies have shown the efficacy of PAA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ...

    Abstract Peracetic acid (PAA) disinfectants are effective against a wide range of pathogenic microorganisms, including bacteria, fungi, and viruses. Several studies have shown the efficacy of PAA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, its efficacy in SARS-CoV-2 variants and the molecular mechanism of action of PAA against SARS-CoV-2 have not been investigated. SARS-CoV-2 infection depends on the recognition and binding of the cell receptor angiotensin-converting enzyme 2 (ACE2) via the receptor-binding domain (RBD) of the spike protein. Here, we demonstrated that PAA effectively suppressed pseudotyped virus infection in the Wuhan type and variants, including Delta and Omicron. Similarly, PAA reduced the authentic viral load of SARS-CoV-2. Computational analysis suggested that the hydroxyl radicals produced by PAA cleave the disulfide bridges in the RBD. Additionally, the PAA treatment decreased the abundance of the Wuhan- and variant-type spike proteins. Enzyme-linked immunosorbent assay showed direct inhibition of RBD-ACE2 interactions by PAA. In conclusion, the PAA treatment suppressed SARS-CoV-2 infection, which was dependent on the inhibition of the interaction between the spike RBD and ACE2 by inducing spike protein destabilization. Our findings provide evidence of a potent disinfection strategy against SARS-CoV-2.
    Keywords SARS-CoV-2 ; peracetic acid ; spike protein ; receptor-binding domain ; ACE2 ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 612
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: [Deposition with DNA Date Bank of Japan (DDBJ); its data format and tools for submitions].

    Satoru, Miyazaki

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme

    2002  Volume 47, Issue 6, Page(s) 733–736

    MeSH term(s) Computational Biology/methods ; Databases, Nucleic Acid ; Internet
    Language Japanese
    Publishing date 2002-05
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 391163-9
    ISSN 0039-9450
    ISSN 0039-9450
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Implication of bidirectional promoters containing duplicated GGAA motifs of mitochondrial function-associated genes

    Fumiaki Uchiumi / Makoto Fujikawa / Satoru Miyazaki / Sei-ichi Tanuma

    AIMS Molecular Science, Vol 1, Iss 1, Pp 1-

    2013  Volume 26

    Abstract: Mitochondria are well known as the primary required organelle in all eukaryotic cells. They have their own mtDNA containing genes that encode tRNAs, rRNAs and a set of functional proteins required for energy (ATP) production. However, almost all (99%) of ...

    Abstract Mitochondria are well known as the primary required organelle in all eukaryotic cells. They have their own mtDNA containing genes that encode tRNAs, rRNAs and a set of functional proteins required for energy (ATP) production. However, almost all (99%) of mitochondrial proteins are encoded by host nuclear genes. Therefore, expression of mitochondrial protein-encoding genes should be regulated similarly to genes that are present in the host nuclear chromosomes. Interestingly, from genomic database assisted surveillance, it was revealed that a lot of mitochondrial function associated protein-encoding genes are oppositely linked in a head-head manner. If the two head-head conjugated genes are regulated by the same transcription factor(s), their expression would be dependent on the direction of transcription machinery that contains RNA polymerase II to execute mRNA synthesis. In this article, we will focus on several examples of the mitochondrial and the partner gene sets and discuss putative functions of transcription factor binding elements in the bidirectional promoters of mitochondrial function-associated genes in chromosomes.
    Keywords bidirectional promoter ; gene loop ; GGAA-motif ; interferon stimulated genes ; mitochondria ; TATA less promote ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2013-12-01T00:00:00Z
    Publisher AIMS Press
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Networking of Biological Resource Centers

    Satoru Miyazaki / Hideaki Sugawara

    Data Science Journal, Vol 1, Iss 2, Pp 229-

    WDCM experiences

    2006  Volume 237

    Abstract: The WFCC-MIRCEN World Data Centre for Microorganisms (WDCM) was set up more than 30 years ago as a data center of the World Federation for Culture Collections (WFCC). It published the World Directory of Collections of Cultures of Microorganisms when it ... ...

    Abstract The WFCC-MIRCEN World Data Centre for Microorganisms (WDCM) was set up more than 30 years ago as a data center of the World Federation for Culture Collections (WFCC). It published the World Directory of Collections of Cultures of Microorganisms when it was established and now provides a portal site for microbial resource centers and their customers by fully utilizing Internet technology. This paper introduces international initiatives on biological resources centers together with the activities of WDCM.
    Keywords Database ; Network ; XML ; Biological resource center ; Microbiology ; Biodiversity ; Science (General) ; Q1-390
    Language English
    Publishing date 2006-01-01T00:00:00Z
    Publisher Ubiquity Press
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Identification of the interaction region between hemagglutinin components of the botulinum toxin complex

    Suzuki, Tomonori / Keita Miyata / Ken Inui / Koichi Niwa / Satoru Miyazaki / Shin-Ichiro Miyashita / Shintaro Hayashi / Tohru Ohyama / Toshihiro Watanabe / Yoshimasa Sagane / Yosuke Kondo

    International journal of biological macromolecules. 2014 Apr., v. 65

    2014  

    Abstract: The large toxin complex (L-TC) produced by Clostridium botulinum is formed from the M-TC (BoNT/NTNHA complex) by conjugation of M-TC with HA-33/HA-17 trimer consists of two HA-33 proteins and a single HA-17 protein. This association is mediated by HA-70, ...

    Abstract The large toxin complex (L-TC) produced by Clostridium botulinum is formed from the M-TC (BoNT/NTNHA complex) by conjugation of M-TC with HA-33/HA-17 trimer consists of two HA-33 proteins and a single HA-17 protein. This association is mediated by HA-70, which interacts with HA-17. The current study aims to identify the regions of the HA-70 molecule that adhere to the HA-33/HA-17 complex. Products from limited proteolysis of HA-70 were resolved by SDS-PAGE and transferred onto PVDF membranes, where they were probed with HA-33/HA-17 in a far-western blot. Among the HA-70 fragments, HA-33/HA-17 bound to those containing at least the C-terminal half of the HA-70 molecule, but not those carrying the N-terminal half. Additional docking simulation analysis indicated that the HA-70 region Gln420-Tyr575 is responsible for binding to HA-17, which is consistent with the far-western blot data. The findings here reveal additional details concerning the three-dimensional structure of the functional HA sub-complex in the botulinum toxin complex.
    Keywords botulinum toxin ; Clostridium botulinum ; hemagglutinins ; polyacrylamide gel electrophoresis ; proteolysis
    Language English
    Dates of publication 2014-04
    Size p. 284-288.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2014.01.052
    Database NAL-Catalogue (AGRICOLA)

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    Zs.B 2374: Show issues Location:
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  7. Article ; Online: Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

    Tadashi Imanishi / Takeshi Itoh / Yutaka Suzuki / Claire O'Donovan / Satoshi Fukuchi / Kanako O Koyanagi / Roberto A Barrero / Takuro Tamura / Yumi Yamaguchi-Kabata / Motohiko Tanino / Kei Yura / Satoru Miyazaki / Kazuho Ikeo / Keiichi Homma / Arek Kasprzyk / Tetsuo Nishikawa / Mika Hirakawa / Jean Thierry-Mieg / Danielle Thierry-Mieg /
    Jennifer Ashurst / Libin Jia / Mitsuteru Nakao / Michael A Thomas / Nicola Mulder / Youla Karavidopoulou / Lihua Jin / Sangsoo Kim / Tomohiro Yasuda / Boris Lenhard / Eric Eveno / Yoshiyuki Suzuki / Chisato Yamasaki / Jun-ichi Takeda / Craig Gough / Phillip Hilton / Yasuyuki Fujii / Hiroaki Sakai / Susumu Tanaka / Clara Amid / Matthew Bellgard / Maria de Fatima Bonaldo / Hidemasa Bono / Susan K Bromberg / Anthony J Brookes / Elspeth Bruford / Piero Carninci / Claude Chelala / Christine Couillault / Sandro J de Souza / Marie-Anne Debily / Marie-Dominique Devignes / Inna Dubchak / Toshinori Endo / Anne Estreicher / Eduardo Eyras / Kaoru Fukami-Kobayashi / Gopal R Gopinath / Esther Graudens / Yoonsoo Hahn / Michael Han / Ze-Guang Han / Kousuke Hanada / Hideki Hanaoka / Erimi Harada / Katsuyuki Hashimoto / Ursula Hinz / Momoki Hirai / Teruyoshi Hishiki / Ian Hopkinson / Sandrine Imbeaud / Hidetoshi Inoko / Alexander Kanapin / Yayoi Kaneko / Takeya Kasukawa / Janet Kelso / Paul Kersey / Reiko Kikuno / Kouichi Kimura / Bernhard Korn / Vladimir Kuryshev / Izabela Makalowska / Takashi Makino / Shuhei Mano / Regine Mariage-Samson / Jun Mashima / Hideo Matsuda / Hans-Werner Mewes / Shinsei Minoshima / Keiichi Nagai / Hideki Nagasaki / Naoki Nagata / Rajni Nigam / Osamu Ogasawara / Osamu Ohara / Masafumi Ohtsubo / Norihiro Okada / Toshihisa Okido / Satoshi Oota / Motonori Ota / Toshio Ota / Tetsuji Otsuki / Dominique Piatier-Tonneau / Annemarie Poustka / Shuang-Xi Ren / Naruya Saitou / Katsunaga Sakai / Shigetaka Sakamoto / Ryuichi Sakate / Ingo Schupp / Florence Servant / Stephen Sherry / Rie Shiba / Nobuyoshi Shimizu / Mary Shimoyama / Andrew J Simpson / Bento Soares / Charles Steward / Makiko Suwa / Mami Suzuki / Aiko Takahashi / Gen Tamiya / Hiroshi Tanaka / Todd Taylor / Joseph D Terwilliger / Per Unneberg / Vamsi Veeramachaneni / Shinya Watanabe / Laurens Wilming / Norikazu Yasuda / Hyang-Sook Yoo / Marvin Stodolsky / Wojciech Makalowski / Mitiko Go / Kenta Nakai / Toshihisa Takagi / Minoru Kanehisa / Yoshiyuki Sakaki / John Quackenbush / Yasushi Okazaki / Yoshihide Hayashizaki / Winston Hide / Ranajit Chakraborty / Ken Nishikawa / Hideaki Sugawara / Yoshio Tateno / Zhu Chen / Michio Oishi / Peter Tonellato / Rolf Apweiler / Kousaku Okubo / Lukas Wagner / Stefan Wiemann / Robert L Strausberg / Takao Isogai / Charles Auffray / Nobuo Nomura / Takashi Gojobori / Sumio Sugano

    PLoS Biology, Vol 2, Iss 6, p e

    2004  Volume 162

    Abstract: The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation ... ...

    Abstract The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
    Keywords Biology (General) ; QH301-705.5
    Subject code 572
    Language English
    Publishing date 2004-06-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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