start-ver=1.4 cd-journal=joma no-vol=189 cd-vols= no-issue=19 article-no= start-page=6945 end-page=6956 dt-received= dt-revised= dt-accepted= dt-pub-year=2007 dt-pub=200710 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Flagellin Glycans from two pathovars of Pseudomonas syringae contain rhamnose in D and L configurations in different ratios and modified 4-amino-4,6-dideoxyglucose en-subtitle= kn-subtitle= en-abstract= kn-abstract=Flagellins from Pseudomonas syringae pv. glycinea race 4 and Pseudomonas syringae pv. tabaci 6605 have been found to be glycosylated. Glycosylation of flagellin is essential for bacterial virulence and is also involved in the determination of host specificity. Flagellin glycans from both pathovars were characterized, and common sites of glycosylation were identified on six serine residues (positions 143, 164, 176, 183, 193, and 201). The structure of the glycan at serine 201 (S201) of flagellin from each pathovar was determined by sugar composition analysis, mass spectrometry, and H-1 and C-13 nuclear magnetic resonance spectroscopy. These analyses showed that the S201 glycans from both pathovars were composed of a common unique trisaccharide consisting of two rhamnosyl (Rha) residues and one modified 4-amino-4,6-dideoxyglucosyl (Qui4N) residue, beta-D-Quip4N(3-hydroxy-1-oxobutyl)2Me-(1 -> 3)-alpha-L-Rhap-(1 -> 2)-alpha-L-Rhap. Furthermore, mass analysis suggests that the glycans on each of the six serine residues are composed of similar trisaccharide units. Determination of the enantiomeric ratio of Rha from the flagellin proteins showed that flagellin from P. syringae pv. tabaci 6605 consisted solely Of L-Rha, whereas P. syringae pv. glycinea race 4 flagellin contained both L-Rha and D-Rha at a molar ratio of about 4:1. Taking these findings together with those from our previous study, we conclude that these flagellin glycan structures may be important for the virulence and host specificity of P. syringae. en-copyright= kn-copyright= en-aut-name=TakeuchiKasumi en-aut-sei=Takeuchi en-aut-mei=Kasumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=OnoHiroshi en-aut-sei=Ono en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=YoshidaMitsuru en-aut-sei=Yoshida en-aut-mei=Mitsuru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=IshiiTadashi en-aut-sei=Ishii en-aut-mei=Tadashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KatohEtsuko en-aut-sei=Katoh en-aut-mei=Etsuko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=TaguchiFumiko en-aut-sei=Taguchi en-aut-mei=Fumiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MikiRyuji en-aut-sei=Miki en-aut-mei=Ryuji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=MurataKatsuyoshi en-aut-sei=Murata en-aut-mei=Katsuyoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=KakuHanae en-aut-sei=Kaku en-aut-mei=Hanae kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=IchinoseYuki en-aut-sei=Ichinose en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= affil-num=1 en-affil= kn-affil=National Institute of Agrobiological Sciences affil-num=2 en-affil= kn-affil=National Food Research Institute affil-num=3 en-affil= kn-affil=National Food Research Institute affil-num=4 en-affil= kn-affil=Forestry and Forest Products Research Institute affil-num=5 en-affil= kn-affil=National Institute of Agrobiological Sciences affil-num=6 en-affil= kn-affil=Graduate School of Natural Science and Technology, Okayama University affil-num=7 en-affil= kn-affil=Graduate School of Natural Science and Technology, Okayama University affil-num=8 en-affil= kn-affil=National Institute of Agrobiological Sciences affil-num=9 en-affil= kn-affil=Faculty of Agriculture, Meiji University affil-num=10 en-affil= kn-affil=Graduate School of Natural Science and Technology, Okayama University en-keyword=INNATE IMMUNE-RESPONSE kn-keyword=INNATE IMMUNE-RESPONSE en-keyword=TOLL-LIKE RECEPTOR-5 kn-keyword=TOLL-LIKE RECEPTOR-5 en-keyword=PV. TABACI kn-keyword=PV. TABACI en-keyword=POSTTRANSLATIONAL MODIFICATION kn-keyword=POSTTRANSLATIONAL MODIFICATION en-keyword=BACTERIAL FLAGELLIN kn-keyword=BACTERIAL FLAGELLIN en-keyword=STRUCTURAL-ANALYSIS kn-keyword=STRUCTURAL-ANALYSIS en-keyword=AMINO-ACIDS kn-keyword=AMINO-ACIDS en-keyword=GLYCOSYLATION kn-keyword=GLYCOSYLATION en-keyword=AERUGINOSA kn-keyword=AERUGINOSA en-keyword=IDENTIFICATION kn-keyword=IDENTIFICATION END start-ver=1.4 cd-journal=joma no-vol=188 cd-vols= no-issue=24 article-no= start-page=8376 end-page=8384 dt-received= dt-revised= dt-accepted= dt-pub-year=2006 dt-pub=200612 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=A homologue of the 3-oxoacyl-(acyl carrier protein) synthase III gene located in the glycosylation island of Pseudomonas syringae pv. tabaci regulates virulence factors via N-acyl homoserine lactone and fatty acid synthesis en-subtitle= kn-subtitle= en-abstract= kn-abstract=Pseudomonas syringae pv. tabaci 6605 possesses a genetic region involved in flagellin glycosylation. This region is composed of three open reading frames: orf1, orf2, and orf3. Our previous study revealed that orf1 and orf2 encode glycosyltransferases; on the other hand, orf3 has no role in posttranslational modification of flagellin. Although the function of Orf3 remained unclear, an orf3 deletion mutant (Delta orf3 mutant) had reduced virulence on tobacco plants. Orf3 shows significant homology to a 3-oxoacyl-(acyl carrier protein) synthase III in the fatty acid elongation cycle. The Delta orf3 mutant had a significantly reduced ability to form acyl homoserine lactones (AHLs), which are quorum-sensing molecules, suggesting that Orf3 is required for AHL synthesis. In comparison with the wild-type strain, swarming motility, biosurfactant production, and tolerance to H2O2 and antibiotics were enhanced in the Delta orf3 mutant. A scanning electron micrograph of inoculated bacteria on the tobacco leaf surface revealed that there is little extracellular polymeric substance matrix surrounding the cells in the Delta orf3 mutant. The phenotypes of the Delta orf3 mutant and an AHL synthesis (Delta psyI) mutant were similar, although the mutant-specific characteristics were more extreme in the Delta orf3 mutant. The swarming motility of the Delta orf3 mutant was greater than that of the Delta psyI mutant. This was attributed to the synergistic effects of the overproduction of biosurfactants and/or alternative fatty acid metabolism in the Delta orf3 mutant. Furthermore, the amounts of iron and biosurfactant seem to be involved in biofilm development under quorum-sensing regulation in P. syringae pv. tabaci 6605. en-copyright= kn-copyright= en-aut-name=TaguchiFumiko en-aut-sei=Taguchi en-aut-mei=Fumiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=OgawaYujiro en-aut-sei=Ogawa en-aut-mei=Yujiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TakeuchiKasumi en-aut-sei=Takeuchi en-aut-mei=Kasumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SuzukiTomoko en-aut-sei=Suzuki en-aut-mei=Tomoko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=ToyodaKazuhiro en-aut-sei=Toyoda en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=ShiraishiTomonori en-aut-sei=Shiraishi en-aut-mei=Tomonori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=IchinoseYuki en-aut-sei=Ichinose en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=The Graduate School of Natural Science and Technology, Okayama University affil-num=2 en-affil= kn-affil=The Graduate School of Natural Science and Technology, Okayama University affil-num=3 en-affil= kn-affil=The Graduate School of Natural Science and Technology, Okayama University affil-num=4 en-affil= kn-affil=The Graduate School of Natural Science and Technology, Okayama University affil-num=5 en-affil= kn-affil=The Graduate School of Natural Science and Technology, Okayama University affil-num=6 en-affil= kn-affil=The Graduate School of Natural Science and Technology, Okayama University affil-num=7 en-affil= kn-affil=The Graduate School of Natural Science and Technology, Okayama University en-keyword=TO-CELL SIGNALS kn-keyword=TO-CELL SIGNALS en-keyword=AERUGINOSA kn-keyword=AERUGINOSA en-keyword=FLAGELLIN kn-keyword=FLAGELLIN en-keyword=BIOFILMS kn-keyword=BIOFILMS en-keyword=MOTILITY kn-keyword=MOTILITY en-keyword=IRON kn-keyword=IRON en-keyword=IDENTIFICATION kn-keyword=IDENTIFICATION en-keyword=SIDEROPHORES kn-keyword=SIDEROPHORES en-keyword=SPECIFICITY kn-keyword=SPECIFICITY en-keyword=FLUORESCENT kn-keyword=FLUORESCENT END start-ver=1.4 cd-journal=joma no-vol=48 cd-vols= no-issue=11 article-no= start-page=4283 end-page=4286 dt-received= dt-revised= dt-accepted= dt-pub-year=2010 dt-pub=201009 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Cholera Toxin Production by the El Tor Variant of Vibrio cholerae O1 Compared to Prototype El Tor and Classical Biotypes en-subtitle= kn-subtitle= en-abstract= kn-abstract=Vibrio cholerae O1 El Tor variant strains produced much more cholera toxin than did prototype El Tor strains. The amount of cholera toxin produced by El Tor variant strains both in vitro and in vivo was more or less equivalent to that produced by classical strains. en-copyright= kn-copyright= en-aut-name=Ghosh-BanerjeeJ en-aut-sei=Ghosh-Banerjee en-aut-mei=J kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=SenohM en-aut-sei=Senoh en-aut-mei=M kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TakahashiT en-aut-sei=Takahashi en-aut-mei=T kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=HamabataT en-aut-sei=Hamabata en-aut-mei=T kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=BarmanS en-aut-sei=Barman en-aut-mei=S kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KoleyH en-aut-sei=Koley en-aut-mei=H kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MukhopadhyayA. K en-aut-sei=Mukhopadhyay en-aut-mei=A. K kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=RamamurthyT en-aut-sei=Ramamurthy en-aut-mei=T kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=ChatterjeeS en-aut-sei=Chatterjee en-aut-mei=S kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=AsakuraM en-aut-sei=Asakura en-aut-mei=M kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=YamasakiS en-aut-sei=Yamasaki en-aut-mei=S kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=NairG. B en-aut-sei=Nair en-aut-mei=G. B kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=TakedaY en-aut-sei=Takeda en-aut-mei=Y kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= affil-num=1 en-affil= kn-affil=National Institute of Cholera and Enteric Diseases affil-num=2 en-affil= kn-affil=Collaborative Research Center of Okayama University for Infectious Diseases in India affil-num=3 en-affil= kn-affil=Collaborative Research Center of Okayama University for Infectious Diseases in India affil-num=4 en-affil= kn-affil=Research Institute, National Center for Global Health and Medicine affil-num=5 en-affil= kn-affil=National Institute of Cholera and Enteric Diseases affil-num=6 en-affil= kn-affil=National Institute of Cholera and Enteric Diseases affil-num=7 en-affil= kn-affil=National Institute of Cholera and Enteric Diseases affil-num=8 en-affil= kn-affil=National Institute of Cholera and Enteric Diseases affil-num=9 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Osaka Prefecture University affil-num=10 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Osaka Prefecture University affil-num=11 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Osaka Prefecture University affil-num=12 en-affil= kn-affil=National Institute of Cholera and Enteric Diseases affil-num=13 en-affil= kn-affil=Collaborative Research Center of Okayama University for Infectious Diseases in India END start-ver=1.4 cd-journal=joma no-vol=50 cd-vols= no-issue=4 article-no= start-page=1308 end-page=1312 dt-received= dt-revised= dt-accepted= dt-pub-year=2012 dt-pub=201204 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Real-Time PCR-Based Mismatch Amplification Mutation Assay for Specific Detection of CS6-Expressing Allelic Variants of Enterotoxigenic Escherichia coli and Its Application in Assessing Diarrheal Cases and Asymptomatic Controls en-subtitle= kn-subtitle= en-abstract= kn-abstract=Enterotoxigenic Escherichia coli (ETEC) expressing the colonization factor CS6 is widespread in many developing countries, including India. The different allelic variants of CS6, caused by point mutations in its structural genes, cssA and cssB, are designated AIBI, AIIBII, AIIIBI, AIBII, and AIIIBII. A simple, reliable, and specific mismatch amplification mutation assay based on real-time quantitative PCR (MAMA-qPCR) was developed for the first time for the detection of CS6-expressing ETEC, along with the identification of allelic variations. The assay was based on mismatched nucleotide incorporation at the penultimate base at the 3' ends of the reverse primers specific for cssA and cssB and was validated using 38 CS6-expressing ETEC isolates. This strategy was effective in detecting all the alleles containing single-nucleotide polymorphisms. Using MAMA-qPCR, we also tested CS6 allelic variants in 145 ETEC isolates from children with acute diarrhea and asymptomatic infections, with the latter serving as controls. We observed that the AIBI and AIIIBI allelic variants were mostly associated with cases rather than controls, whereas the AIIBII variants were detected mostly in controls. In addition, the AIBI and AIIIBI alleles were frequently associated with ETEC harboring the heat-stable toxin gene (est) alone or with the heat-labile toxin gene (elt), whereas the AIIBII allele was predominant in ETEC isolates harboring the elt gene. This study may help in understanding the association of allelic variants in CS6-expressing ETEC with the clinical features of diarrhea, as well as in ETEC vaccine studies. en-copyright= kn-copyright= en-aut-name=SabuiSubrata en-aut-sei=Sabui en-aut-mei=Subrata kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=DuttaSanjucta en-aut-sei=Dutta en-aut-mei=Sanjucta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=DebnathAnusuya en-aut-sei=Debnath en-aut-mei=Anusuya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=GhoshAvishek en-aut-sei=Ghosh en-aut-mei=Avishek kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=HamabataT. en-aut-sei=Hamabata en-aut-mei=T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=RajendranK. en-aut-sei=Rajendran en-aut-mei=K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=RamamurthyT. en-aut-sei=Ramamurthy en-aut-mei=T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=NataroJames P. en-aut-sei=Nataro en-aut-mei=James P. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=SurDipika en-aut-sei=Sur en-aut-mei=Dipika kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=LevineMyron M. en-aut-sei=Levine en-aut-mei=Myron M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=ChatterjeeNabendu Sekhar en-aut-sei=Chatterjee en-aut-mei=Nabendu Sekhar kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= affil-num=1 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=2 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=3 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=4 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=5 en-affil= kn-affil=Natl Ctr Global Hlth & Med affil-num=6 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=7 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=8 en-affil= kn-affil=Univ Virginia, Sch Med, Dept Pediat affil-num=9 en-affil= kn-affil=Natl Inst Cholera & Enter Dis, Calcutta affil-num=10 en-affil= kn-affil=Univ Maryland, Sch Med, Ctr Vaccine Dev affil-num=11 en-affil= kn-affil=Natl Inst Cholera & Enter Dis END start-ver=1.4 cd-journal=joma no-vol=50 cd-vols= no-issue=5 article-no= start-page=1733 end-page=1736 dt-received= dt-revised= dt-accepted= dt-pub-year=2012 dt-pub=201205 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Development and Evaluation of a PCR Assay for Tracking the Emergence and Dissemination of Haitian Variant ctxB in Vibrio cholerae O1 Strains Isolated from Kolkata, India en-subtitle= kn-subtitle= en-abstract= kn-abstract=A PCR-based assay was developed to discriminate the classical, El Tor, and Haitian types of ctxB alleles. Our retrospective study using this newly developed PCR showed that Haitian ctxB first appeared in Kolkata during April 2006, and 93.3% of strains isolated during 2011 carried the new allele. Dendrogram analysis showed a pulsed-field gel electrophoresis (PFGE) pattern of the new variant strains isolated recently that was distinct from the PFGE pattern of the strains carrying classical ctxB that closely matched the 2006 to 2007 variant strains. en-copyright= kn-copyright= en-aut-name=NahaArindam en-aut-sei=Naha en-aut-mei=Arindam kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=PazhaniG. P. en-aut-sei=Pazhani en-aut-mei=G. P. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=GangulyMou en-aut-sei=Ganguly en-aut-mei=Mou kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=GhoshSantanu en-aut-sei=Ghosh en-aut-mei=Santanu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=RamamuranthyT. en-aut-sei=Ramamuranthy en-aut-mei=T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=NandyRanjan K. en-aut-sei=Nandy en-aut-mei=Ranjan K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=NairG. Balakrish en-aut-sei=Nair en-aut-mei=G. Balakrish kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=TakedaYoshifumi en-aut-sei=Takeda en-aut-mei=Yoshifumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=MukhopadhyayAsish K. en-aut-sei=Mukhopadhyay en-aut-mei=Asish K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=2 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=3 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=4 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=5 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=6 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=7 en-affil= kn-affil=Natl Inst Cholera & Enter Dis affil-num=8 en-affil= kn-affil=Okayama Univ Infect Dis NICED, Collaborat Res Ctr affil-num=9 en-affil= kn-affil=Natl Inst Cholera & Enter Dis END start-ver=1.4 cd-journal=joma no-vol=52 cd-vols= no-issue=2 article-no= start-page=544 end-page=548 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=201402 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Necessity for Reassessment of Patients with Serogroup 2 Hepatitis C Virus (HCV) and Undetectable Serum HCV RNA en-subtitle= kn-subtitle= en-abstract= kn-abstract=We encountered a patient positive for anti-hepatitis C virus (HCV) whose serum HCV RNA was undetectable with the Roche AmpliPrep/Cobas TaqMan HCV assay (CAP/CTM) version 1 but showed a high viral load with the Abbott RealTime HCV assay (ART). Discrepancies in the detectability of serum HCV RNA were investigated among 891 consecutive patients who were positive for anti-HCV. Specific nucleotide variations causing the undetectability of HCV RNA were determined and confirmed by synthesizing RNA coding those variations. Serum samples with the discrepancies were also reassessed by CAP/CTM version 2. Among the 891 anti-HCV-positive patients, 4 patients had serum HCV RNA levels that were undetectable by CAP/CTM version 1 despite having levels of > 5 log IU/ml that were detected by ART. All four patients had HCV genotype 2a and high titers of anti-HCV. Sequencing of the HCV 5' noncoding regions revealed 2 common variations, A at nucleotide (nt) 145 and T at nt 151. Synthesized RNAs of the HCV 5' noncoding region with standard (NCR145G151C) and variant nucleotides at nt 145 and nt 151 were quantified with CAP/CTM. RNAs of NCR145G151C and NCR145G151T were quantifiable with CAP/CTM version 1, while those of NCR145A151T and NCR145A151C went undetected. The substitution from G to A at nt 145 specifically conferred this undetectability, while this undetectability was reverted in synthesized HCV RNA with correction of this variation. Reassessment of these samples by CAP/CTM version 2 resulted in similar levels of HCV RNA being detected by ART. We conclude that HCV patients with undetectable HCV RNA by CAP/CTM version 1 should be reassessed for viral quantification. en-copyright= kn-copyright= en-aut-name=MoritouYuki en-aut-sei=Moritou en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IkedaFusao en-aut-sei=Ikeda en-aut-mei=Fusao kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TakeuchiYasuto en-aut-sei=Takeuchi en-aut-mei=Yasuto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SekiHiroyuki en-aut-sei=Seki en-aut-mei=Hiroyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=NanbaShintaro en-aut-sei=Nanba en-aut-mei=Shintaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=IwasakiYoshiaki en-aut-sei=Iwasaki en-aut-mei=Yoshiaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=YamamotoKazuhide en-aut-sei=Yamamoto en-aut-mei=Kazuhide kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=Okayama Univ, Dept Gastroenterol & Hepatol, Grad Sch Med Dent & Pharmaceut Sci affil-num=2 en-affil= kn-affil=Okayama Univ, Dept Gastroenterol & Hepatol, Grad Sch Med Dent & Pharmaceut Sci affil-num=3 en-affil= kn-affil=Okayama Univ, Dept Gastroenterol & Hepatol, Grad Sch Med Dent & Pharmaceut Sci affil-num=4 en-affil= kn-affil=Okayama Univ, Dept Gastroenterol & Hepatol, Grad Sch Med Dent & Pharmaceut Sci affil-num=5 en-affil= kn-affil=Okayama Univ, Dept Gastroenterol & Hepatol, Grad Sch Med Dent & Pharmaceut Sci affil-num=6 en-affil= kn-affil=Okayama Univ, Hlth Serv Ctr affil-num=7 en-affil= kn-affil=Okayama Univ, Dept Gastroenterol & Hepatol, Grad Sch Med Dent & Pharmaceut Sci END start-ver=1.4 cd-journal=joma no-vol=5 cd-vols= no-issue=41 article-no= start-page=e01030-17 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2017 dt-pub=201710 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Chloroplast genome sequences of seven strains of bloom-forming raphidophyte, Heterosigma akashiwo en-subtitle= kn-subtitle= en-abstract= kn-abstract= We report here the complete chloroplast genome sequences of seven strains of the bloom-forming raphidophyte Heterosigma akashiwo. These ~160-kb sequences contain 124 protein-, 6 rRNA-, and 34 tRNA-coding sequences. Notable sequence variations were observed among these seven sequenced and two previously characterized strains. en-copyright= kn-copyright= en-aut-name=SeoaneSergio en-aut-sei=Seoane en-aut-mei=Sergio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HyodoKiwamu en-aut-sei=Hyodo en-aut-mei=Kiwamu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=UekiShoko en-aut-sei=Ueki en-aut-mei=Shoko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= affil-num=1 en-affil=Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU) kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= END start-ver=1.4 cd-journal=joma no-vol=28 cd-vols= no-issue=7 article-no= start-page=2391 end-page=2413 dt-received= dt-revised= dt-accepted= dt-pub-year=2008 dt-pub=200804 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Novel transcription-factor-like function of human matrix metalloproteinase 3 regulating the CTGF/CCN2 gene en-subtitle= kn-subtitle= en-abstract= kn-abstract=@Matrix metalloproteinase 3 (MMP3) is well known as a secretory endopeptidase that degrades extracellular matrices. Recent reports indicated the presence of MMPs in the nucleus (A. J. Kwon et al., FASEB J. 18:690-692, 2004); however, its function has not been well investigated. Here, we report a novel function of human nuclear MMP3 as a trans regulator of connective tissue growth factor (CCN2/CTGF). Initially, we cloned MMP3 cDNA as a DNA-binding factor for the CCN2/CTGF gene. An interaction between MMP3 and transcription enhancer dominant in chondrocytes (TRENDIC) in the CCN2/CTGF promoter was confirmed by a gel shift assay and chromatin immunoprecipitation. The CCN2/CTGF promoter was activated by overexpressed MMP3, whereas a TRENDIC mutant promoter lost the response. Also, the knocking down of MMP3 suppressed CCN2/CTGF expression. By cytochemical and histochemical analyses, MMP3 was detected in the nuclei of chondrocytic cells in culture and also in the nuclei of normal and osteoarthritic chondrocytes in vivo. The nuclear translocation of externally added recombinant MMP3 and six putative nuclear localization signals in MMP3 also were shown. Furthermore, we determined that heterochromatin protein gamma coordinately regulates CCN2/CTGF by interacting with MMP3. The involvement of this novel role of MMP3 in the development, tissue remodeling, and pathology of arthritic diseases through CCN2/CTGF regulation thus is suggested. en-copyright= kn-copyright= en-aut-name=EguchiTakanori en-aut-sei=Eguchi en-aut-mei=Takanori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=KubotaSatoshi en-aut-sei=Kubota en-aut-mei=Satoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=KawataKazumi en-aut-sei=Kawata en-aut-mei=Kazumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=MukudaiYoshiki en-aut-sei=Mukudai en-aut-mei=Yoshiki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=UeharaJunji en-aut-sei=Uehara en-aut-mei=Junji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=OhgawaraToshihiro en-aut-sei=Ohgawara en-aut-mei=Toshihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=IbaragiSoichiro en-aut-sei=Ibaragi en-aut-mei=Soichiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=SasakiAkira en-aut-sei=Sasaki en-aut-mei=Akira kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=KubokiTakuo en-aut-sei=Kuboki en-aut-mei=Takuo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=TakigawaMasaharu en-aut-sei=Takigawa en-aut-mei=Masaharu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= affil-num=1 en-affil=Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=2 en-affil=Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=3 en-affil=Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=4 en-affil=Bio-Dental Research Center, Okayama University Dental School kn-affil= affil-num=5 en-affil=Department of Oral & Maxillofacial Rehabilitation, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=6 en-affil=Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=7 en-affil=Department of Oral & Maxillofacial Surgery & Biopathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=8 en-affil=Department of Oral & Maxillofacial Surgery & Biopathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=9 en-affil=Department of Oral & Maxillofacial Rehabilitation, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= affil-num=10 en-affil=Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences kn-affil= END start-ver=1.4 cd-journal=joma no-vol=51 cd-vols= no-issue=3 article-no= start-page=1040 end-page=1045 dt-received= dt-revised= dt-accepted= dt-pub-year=2013 dt-pub=201303 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Molecular Characterization of High-Level-Cholera-Toxin-Producing El Tor Variant Vibrio cholerae Strains in the Zanzibar Archipelago of Tanzania en-subtitle= kn-subtitle= en-abstract= kn-abstract= Analysis of 1,180 diarrheal stool samples in Zanzibar detected 247 Vibrio cholerae O1, Ogawa strains in 2009. Phenotypic traits and PCR-based detection of rstR, rtxC, and tcpA alleles showed that they belonged to the El Tor biotype. Genetic analysis of ctxB of these strains revealed that they were classical type, and production of classical cholera toxin B (CTB) was confirmed by Western blotting. These strains produced more CT than the prototype El Tor and formed a separate cluster by pulsed-field gel electrophoresis (PFGE) analysis. en-copyright= kn-copyright= en-aut-name=NahaA. en-aut-sei=Naha en-aut-mei=A. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ChowdhuryG. en-aut-sei=Chowdhury en-aut-mei=G. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=Ghosh-BanerjeeJ. en-aut-sei=Ghosh-Banerjee en-aut-mei=J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SenohM. en-aut-sei=Senoh en-aut-mei=M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TakahashiT. en-aut-sei=Takahashi en-aut-mei=T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=LeyB. en-aut-sei=Ley en-aut-mei=B. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=ThriemerK. en-aut-sei=Thriemer en-aut-mei=K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=DeenJ. en-aut-sei=Deen en-aut-mei=J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=SeidleinL. V. en-aut-sei=Seidlein en-aut-mei=L. V. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=AliS. M. en-aut-sei=Ali en-aut-mei=S. M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=KhatibA. en-aut-sei=Khatib en-aut-mei=A. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=RamamurthyT. en-aut-sei=Ramamurthy en-aut-mei=T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=NandyR. K. en-aut-sei=Nandy en-aut-mei=R. K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= en-aut-name=NairG. B. en-aut-sei=Nair en-aut-mei=G. B. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=14 ORCID= en-aut-name=TakedaY. en-aut-sei=Takeda en-aut-mei=Y. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=15 ORCID= en-aut-name=MukhopadhyayA. K. en-aut-sei=Mukhopadhyay en-aut-mei=A. K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=16 ORCID= affil-num=1 en-affil=1National Institute of Cholera and Enteric Diseases kn-affil= affil-num=2 en-affil=1National Institute of Cholera and Enteric Diseases kn-affil= affil-num=3 en-affil=1National Institute of Cholera and Enteric Diseases kn-affil= affil-num=4 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases at NICED, kn-affil= affil-num=5 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases at NICED, kn-affil= affil-num=6 en-affil=The International Vaccine Institute kn-affil= affil-num=7 en-affil=The International Vaccine Institute kn-affil= affil-num=8 en-affil=The International Vaccine Institute kn-affil= affil-num=9 en-affil=Menzies School of Health Research kn-affil= affil-num=10 en-affil=Ministry of Health and Social Welfare kn-affil= affil-num=11 en-affil=Ministry of Health and Social Welfare kn-affil= affil-num=12 en-affil=1National Institute of Cholera and Enteric Diseases kn-affil= affil-num=13 en-affil=1National Institute of Cholera and Enteric Diseases kn-affil= affil-num=14 en-affil=1National Institute of Cholera and Enteric Diseases kn-affil= affil-num=15 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases at NICED, kn-affil= affil-num=16 en-affil=1National Institute of Cholera and Enteric Diseases kn-affil= en-keyword=Vibrio cholerae kn-keyword=Vibrio cholerae en-keyword=ctxB kn-keyword=ctxB en-keyword=Cholera kn-keyword=Cholera en-keyword=PFGE kn-keyword=PFGE END start-ver=1.4 cd-journal=joma no-vol=52 cd-vols= no-issue=3 article-no= start-page=1020 end-page=1021 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=201403 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Haitian variant tcpA in Vibrio cholerae O1 El Tor strains in Kolkata, India en-subtitle= kn-subtitle= en-abstract= kn-abstract= en-copyright= kn-copyright= en-aut-name=GhoshPriyanka en-aut-sei=Ghosh en-aut-mei=Priyanka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=NahaArindam en-aut-sei=Naha en-aut-mei=Arindam kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=BasakSurajit en-aut-sei=Basak en-aut-mei=Surajit kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=GhoshSantanu en-aut-sei=Ghosh en-aut-mei=Santanu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=RamamurthyT. en-aut-sei=Ramamurthy en-aut-mei=T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KoleyHemanta en-aut-sei=Koley en-aut-mei=Hemanta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=K NandyRanjan en-aut-sei=K Nandy en-aut-mei=Ranjan kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=ShinodaSumio en-aut-sei=Shinoda en-aut-mei=Sumio kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=WatanabeHaruo en-aut-sei=Watanabe en-aut-mei=Haruo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=MukhopadhyayAsish K. en-aut-sei=Mukhopadhyay en-aut-mei=Asish K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= affil-num=1 en-affil=Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED) kn-affil= affil-num=2 en-affil=Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED) kn-affil= affil-num=3 en-affil=Department of Molecular Biology & Bioinformatics, Tripura University kn-affil= affil-num=4 en-affil=Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED) kn-affil= affil-num=5 en-affil=Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED) kn-affil= affil-num=6 en-affil=Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED) kn-affil= affil-num=7 en-affil=Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED) kn-affil= affil-num=8 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases at NICED kn-affil= affil-num=9 en-affil=National Institute of Infectious Diseases kn-affil= affil-num=10 en-affil=Division of Bacteriology, National Institute of Cholera and Enteric Diseases (NICED) kn-affil= en-keyword=Cholera kn-keyword=Cholera en-keyword=Vibrio cholerae kn-keyword=Vibrio cholerae en-keyword= tcpA kn-keyword= tcpA en-keyword=El Tor kn-keyword=El Tor END start-ver=1.4 cd-journal=joma no-vol=11 cd-vols= no-issue=3 article-no= start-page=e00450-20 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200526 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Hadaka Virus 1: a Capsidless Eleven-Segmented Positive-Sense Single-Stranded RNA Virus from a Phytopathogenic Fungus, Fusarium oxysporum en-subtitle= kn-subtitle= en-abstract= kn-abstract=The search for viruses infecting fungi, or mycoviruses, has extended our knowledge about the diversity of RNA viruses, as exemplified by the discovery of polymycoviruses, a phylogenetic group of multisegmented RNA viruses with unusual forms. The genomic RNAs of known polymycoviruses, which show a phylogenetic affinity for animal positive-sense single-stranded RNA [(+)RNA] viruses such as caliciviruses, are comprised of four conserved segments with an additional zero to four segments. The double-stranded form of polymycovirus genomic RNA is assumed to be associated with a virally encoded protein (proline-alanine-serine-rich protein [PASrp]) in either of two manners: a capsidless colloidal form or a filamentous encapsidated form. Detailed molecular characterizations of polymycoviruses, however, have been conducted for only a few strains. Here, a novel polymyco-related virus named Hadaka virus 1 (HadV1), from the phytopathogenic fungus Fusarium oxysporum, was characterized. The genomic RNA of HadV1 consisted of an 11-segmented positive-sense RNA with highly conserved terminal nucleotide sequences. HadV1 shared the three conserved segments with known polymycoviruses but lacked the PASrp-encoding segment. Unlike the known polymycoviruses and encapsidated viruses, HadV1 was not pelleted by conventional ultracentrifugation, possibly due to the lack of PASrp. This result implied that HadV1 exists only as a soluble form with naked RNA. Nevertheless, the 11 genomic segments of HadV1 have been stably maintained through host subculturing and conidiation. Taken together, the results of this study revealed a virus with a potential novel virus lifestyle, carrying many genomic segments without typical capsids or PASrp-associated forms. IMPORTANCE Fungi collectively host various RNA viruses. Examples include encapsidated double-stranded RNA (dsRNA) viruses with diverse numbers of genomic segments (from 1 to 12) and capsidless viruses with nonsegmented (+)RNA genomes. Recently, viruses with unusual intermediate features of an infectious entity between encapsidated dsRNA viruses and capsidless (+)RNA viruses were found. They are called polymycoviruses, which typically have four to eight dsRNA genomic segments associated with one of the virus-encoded proteins and are phylogenetically distantly related to animal (+)RNA caliciviruses. Here, we identified a novel virus phylogenetically related to polymycoviruses, from the phytopathogenic fungus Fusarium oxysporum. The virus, termed Hadaka virus 1 (HadV1), has 11 (+)RNA genomic segments, the largest number in known (+)RNA viruses. Nevertheless, HadV1 lacked a typical structural protein of polymycoviruses and was not pelleted by standard ultracentrifugation, implying an unusual capsidless nature of HadV1. This study reveals a potential novel lifestyle of multisegmented RNA viruses. en-copyright= kn-copyright= en-aut-name=SatoYukiyo en-aut-sei=Sato en-aut-mei=Yukiyo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ShamsiWajeeha en-aut-sei=Shamsi en-aut-mei=Wajeeha kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=JamalAtif en-aut-sei=Jamal en-aut-mei=Atif kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=BhattiMuhammad Faraz en-aut-sei=Bhatti en-aut-mei=Muhammad Faraz kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KondoHideki en-aut-sei=Kondo en-aut-mei=Hideki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SuzukiNobuhiro en-aut-sei=Suzuki en-aut-mei=Nobuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Crop Diseases Research Institute, National Agricultural Research Centre kn-affil= affil-num=4 en-affil=Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) kn-affil= affil-num=5 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=6 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=fungal virus kn-keyword=fungal virus en-keyword=polymycovirus kn-keyword=polymycovirus en-keyword=Fusarium oxysporum kn-keyword=Fusarium oxysporum en-keyword=multisegmented kn-keyword=multisegmented en-keyword=RNA virus kn-keyword=RNA virus en-keyword=capsidless kn-keyword=capsidless en-keyword=neo-virus lifestyle kn-keyword=neo-virus lifestyle END start-ver=1.4 cd-journal=joma no-vol=10 cd-vols= no-issue=28 article-no= start-page=e00405-21 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210715 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Complete Genome Sequence of Pseudomonas amygdali pv. tabaci Strain 6605, a Causal Agent of Tobacco Wildfire Disease en-subtitle= kn-subtitle= en-abstract= kn-abstract=Pseudomonas amygdali pv. tabaci strain 6605 is the bacterial pathogen causing tobacco wildfire disease that has been used as a model for elucidating virulence mechanisms. Here, we present the complete genome sequence of P. amygdali pv. tabaci 6605 as a circular chromosome from reads using a PacBio sequencer. en-copyright= kn-copyright= en-aut-name=MatsuiHidenori en-aut-sei=Matsui en-aut-mei=Hidenori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=NishimuraTakafumi en-aut-sei=Nishimura en-aut-mei=Takafumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=AsaiShuta en-aut-sei=Asai en-aut-mei=Shuta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=MasudaSachiko en-aut-sei=Masuda en-aut-mei=Sachiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=ShirasuKen en-aut-sei=Shirasu en-aut-mei=Ken kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=YamamotoMikihiro en-aut-sei=Yamamoto en-aut-mei=Mikihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=NoutoshiYoshiteru en-aut-sei=Noutoshi en-aut-mei=Yoshiteru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=ToyodaKazuhiro en-aut-sei=Toyoda en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=IchinoseYuki en-aut-sei=Ichinose en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Sciences, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Sciences, Okayama University kn-affil= affil-num=3 en-affil=Center for Sustainable Resource Science, RIKEN kn-affil= affil-num=4 en-affil=Center for Sustainable Resource Science, RIKEN kn-affil= affil-num=5 en-affil=Center for Sustainable Resource Science, RIKEN kn-affil= affil-num=6 en-affil=Graduate School of Environmental and Life Sciences, Okayama University kn-affil= affil-num=7 en-affil=Graduate School of Environmental and Life Sciences, Okayama University kn-affil= affil-num=8 en-affil=Graduate School of Environmental and Life Sciences, Okayama University kn-affil= affil-num=9 en-affil=Graduate School of Environmental and Life Sciences, Okayama University kn-affil= END start-ver=1.4 cd-journal=joma no-vol=9 cd-vols= no-issue=1 article-no= start-page=e00077-21 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=202193 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Use of Recombinant Endolysin to Improve Accuracy of Group B Streptococcus Tests en-subtitle= kn-subtitle= en-abstract= kn-abstract=Group B Streptococcus (GBS) causes serious neonatal infection via vertical transmission. The prenatal GBS screening test is performed at the late stage of pregnancy to avoid risks of infection. In this test, enrichment culture is performed, followed by GBS identification. Selective medium is used for the enrichment; however, Enterococcus faecalis, which is a potential contaminant in swab samples, can interfere with the growth of GBS. Such bacterial contamination can lead to false-negative results. Endolysin, a bacteriophage-derived enzyme, degrades peptidoglycan in the bacterial cell wall; it is a promising antimicrobial agent for selectively eliminating specific bacterial genera/species. In this study, we used the recombinant endolysin EG-LYS, which is specific to E. faecalis; the endolysin potentially enriched GBS in the selective culture. First, in the false-negative model (coculture of GBS and E. faecalis, which disabled GBS detection in the subsequent GBS identification test), EG-LYS treatment at 0.1 mg/ml improved GBS detection. Next, we used 548 vaginal swabs to test the efficacy of EG-LYS treatment in improving GBS detection. EG-LYS treatment (0.1 mg/ml) increased the GBS-positive ratio to 17.9%, compared to 15.7% in the control (phosphate-buffered saline [PBS] treatment). In addition, there were an increased number of GBS colonies under EG-LYS treatment in some samples. The results were supported by the microbiota analysis of the enriched cultures. In conclusion, EG-LYS treatment of the enrichment culture potentially improves the accuracy of the prenatal GBS screening test. en-copyright= kn-copyright= en-aut-name=MatsuiHidehito en-aut-sei=Matsui en-aut-mei=Hidehito kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=UchiyamaJumpei en-aut-sei=Uchiyama en-aut-mei=Jumpei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=OgataMasaya en-aut-sei=Ogata en-aut-mei=Masaya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=NasukawaTadahiro en-aut-sei=Nasukawa en-aut-mei=Tadahiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=Takemura-UchiyamaIyo en-aut-sei=Takemura-Uchiyama en-aut-mei=Iyo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KatoShin-ichiro en-aut-sei=Kato en-aut-mei=Shin-ichiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MurakamiHironobu en-aut-sei=Murakami en-aut-mei=Hironobu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=HigashideMasato en-aut-sei=Higashide en-aut-mei=Masato kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=HanakiHideaki en-aut-sei=Hanaki en-aut-mei=Hideaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil=?mura Satoshi Memorial Institute, Kitasato University kn-affil= affil-num=2 en-affil=Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=3 en-affil=School of Veterinary Medicine, Azabu University, Sagamihara kn-affil= affil-num=4 en-affil=School of Veterinary Medicine, Azabu University, Sagamihara kn-affil= affil-num=5 en-affil=School of Veterinary Medicine, Azabu University, Sagamihara kn-affil= affil-num=6 en-affil=Kochi University kn-affil= affil-num=7 en-affil=School of Veterinary Medicine, Azabu University, Sagamihara kn-affil= affil-num=8 en-affil=Kotobiken Medical Laboratories, Inc., Tsukuba kn-affil= affil-num=9 en-affil=?mura Satoshi Memorial Institute, Kitasato University kn-affil= END start-ver=1.4 cd-journal=joma no-vol=95 cd-vols= no-issue=17 article-no= start-page=e00467-21 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=2021810 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Proof of Concept of the Yadokari Nature: a Capsidless Replicase-Encoding but Replication-Dependent Positive-Sense Single-Stranded RNA Virus Hosted by an Unrelated Double-Stranded RNA Virus en-subtitle= kn-subtitle= en-abstract= kn-abstract=Viruses typically encode their own capsids that encase their genomes. However, a capsidless positive-sense single stranded RNA [(+)ssRNA] virus, YkV1, depends on an unrelated double-stranded RNA (dsRNA) virus, YnV1, for encapsidation and replication. en-copyright= kn-copyright= en-aut-name=DasSubha en-aut-sei=Das en-aut-mei=Subha kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=AlamMd Mahfuz en-aut-sei=Alam en-aut-mei=Md Mahfuz kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ZhangRui en-aut-sei=Zhang en-aut-mei=Rui kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=HisanoSakae en-aut-sei=Hisano en-aut-mei=Sakae kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SuzukiNobuhiro en-aut-sei=Suzuki en-aut-mei=Nobuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220830 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Three-Layered Complex Interactions among Capsidless (+)ssRNA Yadokariviruses, dsRNA Viruses, and a Fungus en-subtitle= kn-subtitle= en-abstract= kn-abstract=We have previously discovered a virus neo-lifestyle exhibited by a capsidless positive-sense (+), single-stranded (ss) RNA virus YkV1 (family Yadokariviridae) and an unrelated double-stranded (ds) RNA virus YnV1 (proposed family "Yadonushiviridae") in a phytopathogenic ascomycete, Rosellinia necatrix. YkV1 has been proposed to replicate in the capsid provided by YnV1 as if it were a dsRNA virus and enhance YnV1 replication in return. Recently, viruses related to YkV1 (yadokariviruses) have been isolated from diverse ascomycetous fungi. However, it remains obscure whether such viruses generally show the YkV1-like lifestyle. Here, we identified partner viruses for three distinct yadokariviruses, YkV3, YkV4a, and YkV4b, isolated from R. necatrix that were coinfected with multiple dsRNA viruses phylogenetically distantly related to YnV1. We first established transformants of R. necatrix carrying single yadokarivirus cDNAs and fused them with infectants by single partner candidate dsRNA viruses. Consequently, YkV3 and YkV4s replicated only in the presence of RnMBV3 (family Megabirnaviridae) and RnMTV1 (proposed family "Megatotiviridae"), respectively. The partners were mutually interchangeable between the two YkV4 strains and three RnMTV1 strains but not between other combinations involving YkV1 or YkV3. In contrast to YkV1 enhancing YnV1 accumulation, YkV4s reduced RnMTV1 accumulation to different degrees according to strains. Interestingly, YkV4 rescued the host R. necatrix from impaired growth induced by RnMTV1. YkV3 exerted no apparent effect on its partner (RnMBV3) or host fungus. Overall, we revealed that while yadokariviruses generally require partner dsRNA viruses for replication, each yadokarivirus partners with a different dsRNA virus species in the three diverse families and shows a distinct symbiotic relation in a fungus. IMPORTANCE A capsidless (+)ssRNA virus YkV1 (family Yadokariviridae) highjacks the capsid of an unrelated dsRNA virus YnV1 (proposed family "Yadonushiviridae") in a phytopathogenic ascomycete, while YkV1 trans-enhances YnV1 replication. Herein, we identified the dsRNA virus partners of three yadokariviruses (YkV3, YkV4a, and YkV4b) with genome organization different from YkV1 as being different from YnV1 at the suborder level. Their partners were mutually interchangeable between the two YkV4 strains and three strains of the partner virus RnMTV1 (proposed family "Megatotiviridae") but not between other combinations involving YkV1 or YkV3. Unlike YkV1, YkV4s reduced RnMTV1 accumulation and rescued the host fungus from impaired growth induced by RnMTV1. YkV3 exerted no apparent effect on its partner (RnMBV3, family Megabirnaviridae) or host fungus. These revealed that while each yadokarivirus has a species-specific partnership with a dsRNA virus, yadokariviruses collectively partner extremely diverse dsRNA viruses and show three-layered complex mutualistic/antagonistic interactions in a fungus. en-copyright= kn-copyright= en-aut-name=SatoYukiyo en-aut-sei=Sato en-aut-mei=Yukiyo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HisanoSakae en-aut-sei=Hisano en-aut-mei=Sakae kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=Lopez-HerreraCarlos Jose en-aut-sei=Lopez-Herrera en-aut-mei=Carlos Jose kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KondoHideki en-aut-sei=Kondo en-aut-mei=Hideki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SuzukiNobuhiro en-aut-sei=Suzuki en-aut-mei=Nobuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Instituto de Agricultura Sostenible C.S.I.C., Alameda del Obispo kn-affil= affil-num=4 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=virus-virus interaction kn-keyword=virus-virus interaction en-keyword=RNA viruses kn-keyword=RNA viruses en-keyword=capsidless kn-keyword=capsidless en-keyword=virus macroevolution kn-keyword=virus macroevolution en-keyword=fungal viruses kn-keyword=fungal viruses en-keyword=plant-pathogenic fungi kn-keyword=plant-pathogenic fungi en-keyword=mutualism and parasitism kn-keyword=mutualism and parasitism en-keyword=multilayered interaction kn-keyword=multilayered interaction END start-ver=1.4 cd-journal=joma no-vol=11 cd-vols= no-issue=3 article-no= start-page=e04764-22 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2023 dt-pub=20230426 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Metataxonomic Analysis of the Uterine Microbiota Associated with Low Fertility in Dairy Cows Using Endometrial Tissues Prior to First Artificial Insemination en-subtitle= kn-subtitle= en-abstract= kn-abstract=The deterioration in reproductive performance in association with low fertility leads to significant economic losses on dairy farms. The uterine microbiota has begun to attract attention as a possible cause of unexplained low fertility. We analyzed the uterine microbiota associated with fertility by 16S rRNA gene amplicon sequencing in dairy cows. First, the alpha (Chao1 and Shannon) and beta (unweighted and weighted UniFrac) diversities of 69 cows at four dairy farms that had passed the voluntary waiting period before the first artificial insemination (AI) were analyzed with respect to factors including farm, housing style, feeding management, parity, and AI frequency to conception. Significant differences were observed in the farm, housing style, and feeding management, except parity and AI frequency to conception. The other diversity metrics did not show significant differences in the tested factors. Similar results were obtained for the predicted functional profile. Next, the microbial diversity analysis of 31 cows at a single farm using weighted UniFrac distance matrices revealed a correlation with AI frequency to conception but not with parity. In correlation with AI frequency to conception, the predicted function profile appeared to be slightly modified and a single bacterial taxon, Arcobacter, was detected. The bacterial associations related to fertility were estimated. Considering these, the uterine microbiota in dairy cows can be varied depending on the farm management practices and may become one of the measures for low fertility. en-copyright= kn-copyright= en-aut-name=YagisawaTakuya en-aut-sei=Yagisawa en-aut-mei=Takuya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=UchiyamaJumpei en-aut-sei=Uchiyama en-aut-mei=Jumpei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=Takemura-UchiyamaIyo en-aut-sei=Takemura-Uchiyama en-aut-mei=Iyo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=AndoShun en-aut-sei=Ando en-aut-mei=Shun kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=IchiiOsamu en-aut-sei=Ichii en-aut-mei=Osamu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MurakamiHironobu en-aut-sei=Murakami en-aut-mei=Hironobu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MatsushitaOsamu en-aut-sei=Matsushita en-aut-mei=Osamu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KatagiriSeiji en-aut-sei=Katagiri en-aut-mei=Seiji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Hokkaido Agriculture Mutual Aid Association kn-affil= affil-num=2 en-affil=Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=3 en-affil=Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=4 en-affil=Hokkaido Agriculture Mutual Aid Association kn-affil= affil-num=5 en-affil=Laboratory of Anatomy, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University kn-affil= affil-num=6 en-affil=Laboratory of Infectious Diseases, School of Veterinary Medicine, Azabu University kn-affil= affil-num=7 en-affil=Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=8 en-affil=Laboratory of Theriogenology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University kn-affil= en-keyword=dairy cows kn-keyword=dairy cows en-keyword=low fertility kn-keyword=low fertility en-keyword=uterine microbiota kn-keyword=uterine microbiota en-keyword=microbial diversity kn-keyword=microbial diversity en-keyword=bacterial association kn-keyword=bacterial association END start-ver=1.4 cd-journal=joma no-vol=12 cd-vols= no-issue=12 article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2023 dt-pub=20231214 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Complete genomic sequence of Vibrio fluvialis strain IDH5335 isolated from a patient with diarrhea in Kolkata, India en-subtitle= kn-subtitle= en-abstract= kn-abstract=We isolated a Vibrio fluvialis strain (IDH5335) from a stool sample collected from a patient with diarrhea. In this announcement, we report the complete genomic sequence of this organism, which was obtained by combining Illumina and Oxford Nanopore sequencing data. en-copyright= kn-copyright= en-aut-name=ChowdhuryGoutam en-aut-sei=Chowdhury en-aut-mei=Goutam kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=KitaharaKei en-aut-sei=Kitahara en-aut-mei=Kei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TaniguchiMakoto en-aut-sei=Taniguchi en-aut-mei=Makoto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=UesakaKazuma en-aut-sei=Uesaka en-aut-mei=Kazuma kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=MuzemboBasilua Andre en-aut-sei=Muzembo en-aut-mei=Basilua Andre kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MitraDebmalya en-aut-sei=Mitra en-aut-mei=Debmalya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=OhnoAyumu en-aut-sei=Ohno en-aut-mei=Ayumu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=RamamurthyThandavarayan en-aut-sei=Ramamurthy en-aut-mei=Thandavarayan kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=DuttaShanta en-aut-sei=Dutta en-aut-mei=Shanta kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=MiyoshiShin-ichi en-aut-sei=Miyoshi en-aut-mei=Shin-ichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=MukhopadhyayAsish Kumar en-aut-sei=Mukhopadhyay en-aut-mei=Asish Kumar kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= affil-num=1 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED kn-affil= affil-num=2 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED kn-affil= affil-num=3 en-affil=Oral Microbiome Center, Taniguchi Dental Clinic kn-affil= affil-num=4 en-affil=Graduate School of Bioagricultural Sciences, Nagoya University kn-affil= affil-num=5 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=6 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED kn-affil= affil-num=7 en-affil=Collaborative Research Center of Okayama University for Infectious Diseases in India at ICMR-NICED kn-affil= affil-num=8 en-affil=ICMR-National Institute of Cholera and Enteric Diseases kn-affil= affil-num=9 en-affil=ICMR-National Institute of Cholera and Enteric Diseases kn-affil= affil-num=10 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=11 en-affil=ICMR-National Institute of Cholera and Enteric Diseases kn-affil= en-keyword=Vibrio fluvialis kn-keyword=Vibrio fluvialis en-keyword=diarrhea kn-keyword=diarrhea en-keyword=bacteria kn-keyword=bacteria en-keyword=genome kn-keyword=genome END start-ver=1.4 cd-journal=joma no-vol=9 cd-vols= no-issue=8 article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2024 dt-pub=20240729 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=New lineages of RNA viruses from clinical isolates of Rhizopus microsporus revealed by fragmented and primer-ligated dsRNA sequencing (FLDS) analysis en-subtitle= kn-subtitle= en-abstract= kn-abstract=Rhizopus microsporus is a species in the order Mucorales that is known to cause mucormycosis, but it is poorly understood as a host of viruses. Here, we examined 25 clinical strains of R. microsporus for viral infection with a conventional double-stranded RNA (dsRNA) assay using agarose gel electrophoresis (AGE) and the recently established fragmented and primer-ligated dsRNA sequencing (FLDS) protocol. By AGE, five virus-infected strains were detected. Then, full-length genomic sequences of 12 novel RNA viruses were revealed by FLDS, which were related to the families Mitoviridae, Narnaviridae, and Endornaviridae, ill-defined groups of single-stranded RNA (ssRNA) viruses with similarity to the established families Virgaviridae and Phasmaviridae, and the proposed family "Ambiguiviridae." All the characterized viruses, except a potential phasmavirid with a negative-sense RNA genome, had positive-sense RNA genomes. One virus belonged to a previously established species within the family Mitoviridae, whereas the other 11 viruses represented new species or even new genera. These results show that the fungal pathogen R. microsporus harbors diverse RNA viruses and extend our understanding of the diversity of RNA viruses in the fungal order Mucorales, division Mucoromycota. Identifying RNA viruses from clinical isolates of R. microsporus may expand the repertoire of natural therapeutic agents for mucormycosis in the future. en-copyright= kn-copyright= en-aut-name=Sa'diyahWasiatus en-aut-sei=Sa'diyah en-aut-mei=Wasiatus kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ZhaoYan-Jie en-aut-sei=Zhao en-aut-mei=Yan-Jie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ChibaYuto en-aut-sei=Chiba en-aut-mei=Yuto kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KondoHideki en-aut-sei=Kondo en-aut-mei=Hideki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=SuzukiNobuhiro en-aut-sei=Suzuki en-aut-mei=Nobuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=BanSayaka en-aut-sei=Ban en-aut-mei=Sayaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=YaguchiTakashi en-aut-sei=Yaguchi en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=UrayamaSyun-Ichi en-aut-sei=Urayama en-aut-mei=Syun-Ichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=HagiwaraDaisuke en-aut-sei=Hagiwara en-aut-mei=Daisuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba kn-affil= affil-num=3 en-affil=Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba kn-affil= affil-num=4 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=6 en-affil=Medical Mycology Research Center, Chiba University kn-affil= affil-num=7 en-affil=Medical Mycology Research Center, Chiba University kn-affil= affil-num=8 en-affil=Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba kn-affil= affil-num=9 en-affil=Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba kn-affil= en-keyword=Rhizopus microsporus kn-keyword=Rhizopus microsporus en-keyword=RNA virus kn-keyword=RNA virus en-keyword=diversity kn-keyword=diversity en-keyword=new lineage kn-keyword=new lineage en-keyword=FLDS kn-keyword=FLDS END start-ver=1.4 cd-journal=joma no-vol=99 cd-vols= no-issue=3 article-no= start-page=e02166-24 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2025 dt-pub=20250213 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=A capsidless (+)RNA yadokarivirus hosted by a dsRNA virus is infectious as particles, cDNA, and dsRNA en-subtitle= kn-subtitle= en-abstract= kn-abstract=Capsidless yadokariviruses (members of the order Yadokarivirales) with (+)RNA genomes divert the capsid of their partner icosahedral double-stranded RNA (dsRNA) viruses in different families of the order Ghabrivirales into the replication site. A yadokarivirus, AfSV2, has been reported from a German strain of the ascomycete fungus Aspergillus foetidus coinfected by two dsRNA viruses, a victorivirus (AfSV1, family Pseudototiviridae) and an alternavirus (AfFV, family Alternaviridae). Here, we identified AfSV1 as the partner of AfSV2 in a Japanese A. foetidus strain after showing the infectiousness of AfSV2 in three forms: virus particles (heterocapsid), transforming full-length complementary DNA (cDNA), and purified replicated form (RF) dsRNA that is believed to be inactive as a translational template. Virion transfection of virus-free A. foetidus protoplasts resulted in the generation of two strains infected either by AfSV1 alone or by both AfSV1 and AfSV2. Transformants with AfSV2 full-length cDNA launched AfSV2 infection only in the presence of AfSV1, but not those with AfSV2 RNA-directed RNA polymerase mutant cDNA. The purified fractions containing AfSV2 RF dsRNA also launched infection when transfected into protoplasts infected by AfSV1. Treatment with dsRNA-specific RNase III, but not with proteinase K, S1 nuclease, or DNase I, abolished the infectivity of AfSV2 RF dsRNA. Furthermore, we confirmed the infectiousness of gel-purified AfSV2 RF dsRNA in the presence of AfSV1. Taken together, our results show the unique infectious entity of AfSV2 and the expansion of yadokarivirus partners in the family Pseudototiviridae and provide interesting evolutionary insights. en-copyright= kn-copyright= en-aut-name=FadliMuhammad en-aut-sei=Fadli en-aut-mei=Muhammad kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HisanoSakae en-aut-sei=Hisano en-aut-mei=Sakae kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=NovoaGuy en-aut-sei=Novoa en-aut-mei=Guy kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=Cast?nJos? R. en-aut-sei=Cast?n en-aut-mei=Jos? R. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KondoHideki en-aut-sei=Kondo en-aut-mei=Hideki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SuzukiNobuhiro en-aut-sei=Suzuki en-aut-mei=Nobuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= affil-num=1 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Department of Structure of Macromolecules, Centro Nacional Biotecnolog?a (CNB-CSIC), Campus de Cantoblanco kn-affil= affil-num=4 en-affil=Department of Structure of Macromolecules, Centro Nacional Biotecnolog?a (CNB-CSIC), Campus de Cantoblanco kn-affil= affil-num=5 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=6 en-affil=Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=yadokarivirus kn-keyword=yadokarivirus en-keyword=hetero-encapsidation kn-keyword=hetero-encapsidation en-keyword=partner dsRNA virus kn-keyword=partner dsRNA virus en-keyword=fungal virus kn-keyword=fungal virus en-keyword=Aspergillus foetidus kn-keyword=Aspergillus foetidus en-keyword=neo-lifestyle kn-keyword=neo-lifestyle END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2025 dt-pub=20250410 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Enterobacterial common antigen repeat-unit flippase WzxE is required for Escherichia coli growth under acidic conditions, low temperature, and high osmotic stress conditions en-subtitle= kn-subtitle= en-abstract= kn-abstract=Colanic acid and enterobacterial common antigen (ECA) are cell-surface polysaccharides that are produced by many Escherichia coli isolates. Colanic acid is induced under acidic, low temperature, and high-salt conditions and is important for E. coli resistance to these stresses; however, the role of ECA in these stresses is less clear. Here, we observed that knockout of flippase wzxE, which translocates lipid-linked ECA repeat units from the cytoplasmic side of the inner membrane to the periplasmic side, resulted in the sensitivity of E. coli BW25113 to acidic conditions. The wzxE-knockout mutant showed reduced growth potential and viable counts in vegetable extracts with acidic environments, including cherry tomatoes, carrots, celery, lettuce, and spinach. A double-knockout strain of wzxE and wecF (glycosyltransferase that adds the third-and-final sugar of the lipid-linked ECA repeat unit) was not sensitive to acidic conditions, with similar results obtained for a double-knockout strain of wzxE and wcaJ (glycosyltransferase that initiates colanic acid lipid-linked repeat-unit biosynthesis). The wzxE-knockout mutant was sensitive to low temperatures or high-salt conditions, which induced colanic acid synthesis, and these sensitivities were abolished by the additional knockout of wcaJ. These results suggest that lipid-linked ECA repeat units confer E. coli susceptibility to acidic, low temperatures, and high-salt conditions in a colanic acid-dependent manner and that wzxE suppresses this negative effect. en-copyright= kn-copyright= en-aut-name=YamaguchiSaki en-aut-sei=Yamaguchi en-aut-mei=Saki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IshikawaKazuya en-aut-sei=Ishikawa en-aut-mei=Kazuya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=FurutaKazuyuki en-aut-sei=Furuta en-aut-mei=Kazuyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KaitoChikara en-aut-sei=Kaito en-aut-mei=Chikara kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= en-keyword=wzxE flippase kn-keyword=wzxE flippase en-keyword=enterobacterial common antigen kn-keyword=enterobacterial common antigen en-keyword=low pH kn-keyword=low pH en-keyword=low temperature kn-keyword=low temperature en-keyword=hyperosmotic stress kn-keyword=hyperosmotic stress END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2025 dt-pub=20250501 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Xenopus laevis as an infection model for human pathogenic bacteria en-subtitle= kn-subtitle= en-abstract= kn-abstract=Animal infection models are essential for understanding bacterial pathogenicity and corresponding host immune responses. In this study, we investigated whether juvenile Xenopus laevis could be used as an infection model for human pathogenic bacteria. Xenopus frogs succumbed to intraperitoneal injection containing the human pathogenic bacteria Staphylococcus aureus, Pseudomonas aeruginosa, and Listeria monocytogenes. In contrast, non-pathogenic bacteria Bacillus subtilis and Escherichia coli did not induce mortality in Xenopus frogs. The administration of appropriate antibiotics suppressed mortality caused by S. aureus and P. aeruginosa. Strains lacking the agr locus, cvfA (rny) gene, or hemolysin genes in S. aureus, LIPI-1-deleted mutant of L. monocytogenes, which attenuate virulence within mammals, exhibited reduced virulence in Xenopus frogs compared with their respective wild-type counterparts. Bacterial distribution analysis revealed that S. aureus persisted in the blood, liver, heart, and muscles of Xenopus frogs until death. These results suggested that intraperitoneal injection of human pathogenic bacteria induces sepsis-like symptoms in Xenopus frogs, supporting their use as a valuable animal model for evaluating antimicrobial efficacy and identifying virulence genes in various human pathogenic bacteria. en-copyright= kn-copyright= en-aut-name=KuriuAyano en-aut-sei=Kuriu en-aut-mei=Ayano kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IshikawaKazuya en-aut-sei=Ishikawa en-aut-mei=Kazuya kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TsuchiyaKohsuke en-aut-sei=Tsuchiya en-aut-mei=Kohsuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=FurutaKazuyuki en-aut-sei=Furuta en-aut-mei=Kazuyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KaitoChikara en-aut-sei=Kaito en-aut-mei=Chikara kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= affil-num=1 en-affil=Division of Molecular Biology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=2 en-affil=Division of Molecular Biology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=3 en-affil=Division of Immunology and Molecular Biology, Cancer Research Institute, Kanazawa University kn-affil= affil-num=4 en-affil=Division of Molecular Biology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=5 en-affil=Division of Molecular Biology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University kn-affil= en-keyword=animal infection model kn-keyword=animal infection model en-keyword=Staphylococcus aureus kn-keyword=Staphylococcus aureus en-keyword=Listeria monocytogenes kn-keyword=Listeria monocytogenes en-keyword=Pseudomonas aeruginosa kn-keyword=Pseudomonas aeruginosa en-keyword=antibiotics efficacy kn-keyword=antibiotics efficacy en-keyword=virulence genes kn-keyword=virulence genes en-keyword=hemolysin kn-keyword=hemolysin END