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  1. Article: [Massive nucleotide sequence data analysis reveals the nature of viruses].

    Nakagawa, So

    Uirusu

    2021  Volume 70, Issue 1, Page(s) 45–48

    MeSH term(s) Base Sequence ; Data Analysis ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Viruses/genetics
    Language Japanese
    Publishing date 2021-03-10
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 603272-2
    ISSN 0042-6857
    ISSN 0042-6857
    DOI 10.2222/jsv.70.45
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 266: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Dynamic Evolution of Retroviral Envelope Genes in Egg-Laying Mammalian Genomes.

    Kitao, Koichi / Shoji, Hiyori / Miyazawa, Takayuki / Nakagawa, So

    Molecular biology and evolution

    2023  Volume 40, Issue 5

    Abstract: Independently acquired envelope (env) genes from endogenous retroviruses have contributed to the placental trophoblast cell-cell fusion in therian mammals. Egg-laying mammals (monotremes) are an important sister clade for understanding mammalian ... ...

    Abstract Independently acquired envelope (env) genes from endogenous retroviruses have contributed to the placental trophoblast cell-cell fusion in therian mammals. Egg-laying mammals (monotremes) are an important sister clade for understanding mammalian placental evolution, but the env genes in their genomes have yet to be investigated. Here, env-derived open reading frames (env-ORFs) encoding more than 400 amino acid lengths were searched in the genomes of two monotremes: platypus and echidna. Only two env-ORFs were present in the platypus genome, whereas 121 env-ORFs were found in the echidna genome. The echidna env-ORFs were phylogenetically classified into seven groups named env-Tac1 to -Tac7. Among them, the env-Tac1 group contained only a single gene, and its amino acid sequence showed high similarity to those of the RD114/simian type D retroviruses. Using the pseudotyped virus assay, we demonstrated that the Env-Tac1 protein utilizes echidna sodium-dependent neutral amino acid transporter type 1 and 2 (ASCT1 and ASCT2) as entry receptors. Moreover, the Env-Tac1 protein caused cell-cell fusion in human 293T cells depending on the expression of ASCT1 and ASCT2. These results illustrate that fusogenic env genes are not restricted to placental mammals, providing insights into the evolution of retroviral genes and the placenta.
    MeSH term(s) Animals ; Pregnancy ; Female ; Humans ; Genes, env ; Placenta ; Platypus/genetics ; Tachyglossidae/genetics ; Endogenous Retroviruses ; Gene Products, env/genetics ; Mammals/genetics
    Chemical Substances Gene Products, env
    Language English
    Publishing date 2023-04-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msad090
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2137: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System.

    Kryukov, Kirill / Imanishi, Tadashi / Nakagawa, So

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2632, Page(s) 215–226

    Abstract: With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using ... ...

    Abstract With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using nanopore sequencing data of 16S rRNA genes as an example. GenomeSync is a collection of genome sequences designed to provide easy access to genomic data of the species as demanded. GSTK (genome search toolkit) is a set of scripts for managing local homology searches using genomes obtained from the GenomeSync database. Based on this protocol, nanopore sequencing data analyses of metagenomes and amplicons could be efficiently performed. We also noted reanalysis in conjunction with future developments in nanopore sequencing technology and the accumulation of genome sequencing data.
    MeSH term(s) Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Nanopore Sequencing ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Nanopores
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-02-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2996-3_15
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  5. Article ; Online: Potentially reduced fusogenicity of syncytin-2 in New World monkeys.

    Shoji, Hiyori / Kitao, Koichi / Miyazawa, Takayuki / Nakagawa, So

    FEBS open bio

    2023  Volume 13, Issue 3, Page(s) 459–467

    Abstract: Syncytin-2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin-2 is ... ...

    Abstract Syncytin-2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin-2 is conserved between apes and OWMs, suggesting its functional importance; however, syncytin-2 of common marmosets (Callithrix jacchus) exhibits lower fusogenic activity than those of humans and OWMs in human cell lines. To obtain insight into the functional diversity of syncytin-2 genes in primates, we examined the syncytin-2 gene in New World monkeys (NWMs). We experimentally evaluated the cell fusion ability of syncytin-2 in humans, C. jacchus, and tufted capuchins (Sapajus apella). We found that the cell fusion ability of S. apella was lower than that of human syncytin-2. Chimeric syncytin-2 constructs revealed that the amino acid differences in the surface unit of S. apella syncytin-2 were responsible for the weak cell fusion activity. In addition, genomic sequence analyses of syncytin-2 revealed that the open reading frames (ORFs) of syncytin-2 were highly conserved in seven apes and 22 OWMs; however, the syncytin-2 ORFs of three of 12 NWM species were truncated. Our results suggest that syncytin-2 in several NWMs may be of less importance than in OWMs and apes, and other syncytin-like genes may be required for placental development in various NWM species.
    MeSH term(s) Animals ; Pregnancy ; Humans ; Female ; Placenta/metabolism ; Platyrrhini/metabolism ; Gene Products, env/genetics ; Gene Products, env/chemistry ; Gene Products, env/metabolism ; Hominidae/metabolism
    Chemical Substances syncytin ; Gene Products, env
    Language English
    Publishing date 2023-01-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2651702-4
    ISSN 2211-5463 ; 2211-5463
    ISSN (online) 2211-5463
    ISSN 2211-5463
    DOI 10.1002/2211-5463.13555
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Potentially reduced fusogenicity of syncytin‐2 in New World monkeys

    Hiyori Shoji / Koichi Kitao / Takayuki Miyazawa / So Nakagawa

    FEBS Open Bio, Vol 13, Iss 3, Pp 459-

    2023  Volume 467

    Abstract: Syncytin‐2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin‐2 is ... ...

    Abstract Syncytin‐2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin‐2 is conserved between apes and OWMs, suggesting its functional importance; however, syncytin‐2 of common marmosets (Callithrix jacchus) exhibits lower fusogenic activity than those of humans and OWMs in human cell lines. To obtain insight into the functional diversity of syncytin‐2 genes in primates, we examined the syncytin‐2 gene in New World monkeys (NWMs). We experimentally evaluated the cell fusion ability of syncytin‐2 in humans, C. jacchus, and tufted capuchins (Sapajus apella). We found that the cell fusion ability of S. apella was lower than that of human syncytin‐2. Chimeric syncytin‐2 constructs revealed that the amino acid differences in the surface unit of S. apella syncytin‐2 were responsible for the weak cell fusion activity. In addition, genomic sequence analyses of syncytin‐2 revealed that the open reading frames (ORFs) of syncytin‐2 were highly conserved in seven apes and 22 OWMs; however, the syncytin‐2 ORFs of three of 12 NWM species were truncated. Our results suggest that syncytin‐2 in several NWMs may be of less importance than in OWMs and apes, and other syncytin‐like genes may be required for placental development in various NWM species.
    Keywords endogenous retrovirus ; envelope protein ; New World monkey ; placenta ; syncytin ; Biology (General) ; QH301-705.5
    Subject code 572
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Identification of Genes Associated with Resistance to Persulcatusin, a Tick Defensin from

    Shimoda, So / Ito, Junya / Ando, Tasuke / Tobe, Ryuta / Nakagawa, Kiyotaka / Yoneyama, Hiroshi

    Microorganisms

    2024  Volume 12, Issue 2

    Abstract: Antimicrobial peptides (AMPs) are present in a wide range of plants, animals, and microorganisms. Since AMPs are characterized by their effectiveness against emergent antibiotic-resistant bacteria, they are attracting attention as next-generation ... ...

    Abstract Antimicrobial peptides (AMPs) are present in a wide range of plants, animals, and microorganisms. Since AMPs are characterized by their effectiveness against emergent antibiotic-resistant bacteria, they are attracting attention as next-generation antimicrobial compounds that could solve the problem of drug-resistant bacteria. Persulcatusin (IP), an antibacterial peptide derived from the hard tick
    Language English
    Publishing date 2024-02-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms12020412
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  8. Article: Rare

    Oka, Akira / Hadano, Shinji / Ueda, Mahoko Takahashi / Nakagawa, So / Komaki, Gen / Ando, Tetsuya

    Heliyon

    2024  Volume 10, Issue 8, Page(s) e28643

    Abstract: Eating disorders (EDs) are a type of psychiatric disorder characterized by pathological eating and related behavior and considered to be highly heritable. The purpose of this study was to explore rare variants expected to display biological functions ... ...

    Abstract Eating disorders (EDs) are a type of psychiatric disorder characterized by pathological eating and related behavior and considered to be highly heritable. The purpose of this study was to explore rare variants expected to display biological functions associated with the etiology of EDs. We performed whole exome sequencing (WES) of affected sib-pairs corresponding to disease subtype through their lifetime and their parents. From those results, rare single nucleotide variants (SNVs) concordant with sib-pairs were extracted and estimated to be most deleterious in the examined families. Two non-synonymous SNVs located on corticotropin-releasing hormone receptor 2 (
    Language English
    Publishing date 2024-03-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e28643
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  9. Article ; Online: Potentially reduced fusogenicity of syncytin‐2 in New World monkeys

    Shoji, Hiyori / Kitao, Koichi / Miyazawa, Takayuki / Nakagawa, So

    FEBS Open Bio. 2023 Mar., v. 13, no. 3, p. 459-467

    2023  , Page(s) 459–467

    Abstract: Syncytin‐2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin‐2 is ... ...

    Abstract Syncytin‐2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin‐2 is conserved between apes and OWMs, suggesting its functional importance; however, syncytin‐2 of common marmosets (Callithrix jacchus) exhibits lower fusogenic activity than those of humans and OWMs in human cell lines. To obtain insight into the functional diversity of syncytin‐2 genes in primates, we examined the syncytin‐2 gene in New World monkeys (NWMs). We experimentally evaluated the cell fusion ability of syncytin‐2 in humans, C. jacchus, and tufted capuchins (Sapajus apella). We found that the cell fusion ability of S. apella was lower than that of human syncytin‐2. Chimeric syncytin‐2 constructs revealed that the amino acid differences in the surface unit of S. apella syncytin‐2 were responsible for the weak cell fusion activity. In addition, genomic sequence analyses of syncytin‐2 revealed that the open reading frames (ORFs) of syncytin‐2 were highly conserved in seven apes and 22 OWMs; however, the syncytin‐2 ORFs of three of 12 NWM species were truncated. Our results suggest that syncytin‐2 in several NWMs may be of less importance than in OWMs and apes, and other syncytin‐like genes may be required for placental development in various NWM species.
    Keywords Callithrix jacchus ; Sapajus ; amino acids ; cell fusion ; functional diversity ; genes ; humans ; membrane fusion ; nucleotide sequences ; placenta
    Language English
    Dates of publication 2023-03
    Size p. 459-467
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 2651702-4
    ISSN 2211-5463
    ISSN 2211-5463
    DOI 10.1002/2211-5463.13555
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  10. Article: Monotreme-specific conserved putative proteins derived from retroviral reverse transcriptase.

    Kitao, Koichi / Miyazawa, Takayuki / Nakagawa, So

    Virus evolution

    2022  Volume 8, Issue 2, Page(s) veac084

    Abstract: Endogenous retroviruses (ERVs) have played an essential role in the evolution of mammals. ERV-derived genes are reported in the therians, many of which are involved in placental development; however, the contribution of the ERV-derived genes in ... ...

    Abstract Endogenous retroviruses (ERVs) have played an essential role in the evolution of mammals. ERV-derived genes are reported in the therians, many of which are involved in placental development; however, the contribution of the ERV-derived genes in monotremes, which are oviparous mammals, remains to be uncovered. Here, we conducted a comprehensive search for possible ERV-derived genes in platypus and echidna genomes and identified three reverse transcriptase-like genes named
    Language English
    Publishing date 2022-09-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veac084
    Database MEDical Literature Analysis and Retrieval System OnLINE

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