[Show abstract][Hide abstract] ABSTRACT: In Japan, the emergence of macrolide- and oxytetracycline-resistant strains of
has previously been reported. Here, we describe the draft genome sequence of
strain U-1, isolated in 2011 from a diseased yellowtail in Kagoshima Prefecture. The draft genome does not have any genes responsible for macrolide and tetracycline resistance.
Preview · Article · Feb 2016 · Genome Announcements
[Show abstract][Hide abstract] ABSTRACT: We report the draft genome sequence of Nocardia seriolae strain N-2927 (NBRC 110360), isolated from cultured yellowtail Seriola quinqueradiata. RAST annotation of the genome revealed 117 genes involved in the virulence, disease, and defense subsystem. Eleven of these
genes were predicted as antibiotic resistance genes.
Preview · Article · Mar 2015 · Genome Announcements
[Show abstract][Hide abstract] ABSTRACT: Vaccination with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of Edwardsiella tarda has been demonstrated to have cross-protection against some other bacterial pathogens. We prepared a recombinant protein and pcDNA4 expression vector of GAPDH of E. tarda and injected those to 0-age yellowtail Serbia quinqueradiata to evaluate their protective efficacies against Nocardia seriolae. The 60-d survival rates ranged from 0% to 6.7% among vaccinated and control groups, suggesting that the protein and expression vector of E. tarda GAPDH had no protective effect against nocardiosis. However, the copy numbers of the 16S ribosomal RNA gene of N. seriolae were significantly lower in the gill, kidney, and spleen of vaccinated fish 9 and 18 days post-infection compared with those in the control group that was also challenged with N. seriolae. Additionally, the CC chemokine, major histocompatibility complex class II alpha antigen, interleukin 1 beta, and immunoglobulin M genes were significantly upregulated in the vaccinated groups. Four predicted B-cell epitopes of GAPDH in E. tarda, which may play an important role in cross-protection, differed in amino acid sequences from those of GAPDH in N. seriolae. This may explain the lack of a protective effect of E. tarda GAPDH against N. seriolae.
[Show abstract][Hide abstract] ABSTRACT: Streptococcus parauberis strain SK-417 was isolated from the brain of a diseased Sebastes ventricosus, collected from an aquaculture farm in April 2013 in Kagoshima Prefecture, Japan. The draft genome sequence, obtained with
a 454 GS Junior sequencing system, consists of 33 large contigs of >500 bp, totaling 1,958,836 bp, and has a G+C content of
Preview · Article · May 2014 · Genome Announcements
[Show abstract][Hide abstract] ABSTRACT: Edwardsiella piscicida is a new species discovered within the group of organisms traditionally classified as Edwardsiella tarda. We present draft genome sequences of two variant strains of E. piscicida, JF1305 and RSB1309. Differences in protein-coding sequence between these isolates are associated with virulence, disease,
and defense, suggesting differences in pathogenicity.
Preview · Article · May 2014 · Genome Announcements
[Show abstract][Hide abstract] ABSTRACT: To determine the host cellular gene expression profiles in chronic active Epstein-Barr virus infection (CAEBV), peripheral blood samples were obtained from three patients with CAEBV and investigated using a PCR array analysis that focused on T-cell/B-cell activation. We identified six genes with expression levels that were tenfold higher in CAEBV patients compared with those in healthy controls. These results were verified by quantitative reverse transcription-PCR. We identified four highly upregulated genes, i.e., IL-10, IL-2, IFNGR1, and INHBA. These genes may be involved in inflammatory responses and cell proliferation, and they may contribute to the development and progression of CAEBV.
No preview · Article · May 2014 · Microbes and Infection
[Show abstract][Hide abstract] ABSTRACT: A new cell line named CCF-K104 predominantly consisting of fibroblastic cells showed optimal growth at temperatures from 25 °C to 30 °C. Serial morphological changes in the cells induced by Cyprinid herpesvirus 3 (CyHV-3) included cytoplasmic vacuolar formation, cell rounding and detachment. Mature virions were purified from CyHV-3-infected CCF-K104 cells by sucrose gradient ultracentrifugation and had a typical herpesvirus structure on electron microscopy. Infectious CyHV-3 was produced stably in CCF-K104 cells over 30 viral passages. Our findings showed that CCF-K104 is a useful cell line for isolation and productive replication of CyHV-3. A temperature shift from 25 °C to 15 °C or 35 °C did not allow serial morphological changes as observed at 25 °C for 14 days. Under the same conditions, real-time PCR showed that CyHV-3 was present with low viral DNA loads, suggesting that CyHV-3 may establish latent infection in CCF-K104 cells. Amplification of the left and right terminal repeat sequences of the CyHV-3 genome arranged in a head-to-tail manner was detected by nested PCR following an upshift in temperature from 25 °C to 35 °C. The PCR results suggested that the circular genome may represent a latent form of CyHV-3.
No preview · Article · May 2014 · Journal of Fish Diseases
[Show abstract][Hide abstract] ABSTRACT: To determine the host cellular gene expression profiles in chronic active Epstein–Barr virus infection (CAEBV), peripheral blood samples were obtained from three patients with CAEBV and investigated using a PCR array analysis that focused on T-cell/B-cell activation. We identified six genes with expression levels that were tenfold higher in CAEBV patients compared with those in healthy controls. These results were verified by quantitative reverse transcription-PCR. We identified four highly upregulated genes, i.e., IL-10, IL-2, IFNGR1, and INHBA. These genes may be involved in inflammatory responses and cell proliferation, and they may contribute to the development and progression of CAEBV.
No preview · Article · Jan 2014 · Microbes and Infection
[Show abstract][Hide abstract] ABSTRACT: Most Merkel cell polyomavirus (MCPyV) gene sequences have been reported from Western countries and few data are available for the virus sequences from other geographical areas, especially Asia. Thus, we performed phylogenetic analyses based on the nucleotide sequences of the full-length large T antigen (LT) and viral protein 1 (VP1) genes derived from a variety of cancers in Japanese patients and compared them with sequences from Caucasians. The LT and VP1 gene-based phylogenetic trees identified two main genetic clades. One clade comprised strains isolated from Caucasians, whereas all of the Japanese tumor-derived MCPyV strains belonged to another clade. These findings confirm that most of the MCPyV strains present in Japan form a clade, distinct from Caucasian strains.
Preview · Article · Oct 2013 · Journal of General Virology
[Show abstract][Hide abstract] ABSTRACT: Merkel cell polyomavirus (MCPyV), human polyomaviruses 6 (HPyV6) and 7 (HPyV7) are novel human polyomaviruses. This study investigated their detection rates and DNA loads in various skin cancers from Japanese patients. MCPyV, HPyV6 and HPyV7 were detected in 22.2%, 3.2% and 1.6% of squamous cell carcinomas, 18.0%, 2.0% and 4.0% of basal cell carcinomas, and 19.1%, 4.3% and 4.3% of melanomas, respectively. Quantitative real-time polymerase chain reaction showed that their DNA loads were low. These findings provide the first evidence of the prevalence of HPyV6 and HPyV7 in skin cancers in Asia. Nucleotide differences were found in the large T-sequenced region between Japanese and North American isolates: a nucleotide substitution of A to G for HPyV6; and a nucleotide substitution of T to C and the insertion of a gap for HPyV7. This suggested that two genotypes of HPyV6 and HPyV7 would be present and associated with geographical origin.
No preview · Article · May 2013 · The Journal of Dermatology
[Show abstract][Hide abstract] ABSTRACT: Background:
We searched for a viral aetiology for non-small cell lung cancer (NSCLC), focusing on Merkel cell polyomavirus (MCPyV).
We analysed 112 Japanese cases of NSCLC for the presence of the MCPyV genome and the expressions of RNA transcripts and MCPyV-encoded antigen. We also conducted the first analysis of the molecular features of MCPyV in lung cancers.
PCR revealed that 9 out of 32 squamous cell carcinomas (SCCs), 9 out of 45 adenocarcinomas (ACs), 1 out of 32 large-cell carcinomas, and 1 out of 3 pleomorphic carcinomas were positive for MCPyV DNA. Some MCPyV DNA-positive cancers expressed large T antigen (LT) RNA transcripts. Immunohistochemistry showed that MCPyV LT antigen was expressed in the tumour cells. The viral integration sites were identified in one SCC and one AC. One had both episomal and integrated/truncated forms. The other carried an integrated MCPyV genome with frameshift mutations in the LT gene.
We have demonstrated the expression of a viral oncoprotein, the presence of integrated MCPyV, and a truncated LT gene with a preserved retinoblastoma tumour-suppressor protein-binding domain in NSCLCs. Although the viral prevalence was low, the tumour-specific molecular signatures support the possibility that MCPyV is partly associated with the pathogenesis of NSCLC in a subset of patients.
Preview · Article · Jan 2013 · British Journal of Cancer
[Show abstract][Hide abstract] ABSTRACT: In Japan, a Mycobacterium marinum‐like mycobacterium was isolated from the yellowtail, Seriola quinqueradiata. The species was identified as M. marinum by a commercial mycobacterial DNA‐DNA hybridization kit. Nevertheless, PCR restriction analysis of the DNA of its RNA polymerase β‐subunit gene definitively showed that this Mycobacterium sp. was M. ulcerans. PCR analysis revealed the genotypic characteristics of M. ulcerans in the Mycobacterium sp., only the mup053 gene sequence being absent, as has been found previously in other piscine mycobacteria such as M. marinum strains DL240490 and DL045 and M. pseudoshottsii. With one exception, this Mycobacterium sp. and M. pseudoshottsii had identical 16S rRNA gene sequences, which is also probably true of M. marinum strains DL240490 and DL045. Similarly, according to comparisons of the 16S rRNA gene, ITS region, and hsp65 gene sequences, this Mycobacterium sp. is more closely related to M. pseudoshottsii than to M. ulcerans or M. marinum. A PCR product of approximately 2000 bp was amplified from region of difference 9 in the Mycobacterium sp. The nucleotide sequence revealed insertion of IS2404, the sequence of which is 1366 bp long. The novel single nucleotide polymorphisms identified in this region distinguished this Mycobacterium sp. from M. marinum strain DL240490 and M. pseudoshottsii. The present findings raise the possibility that these species have a common ancestor. Further studies are required to improve our understanding of the relationship between their geographical origin and genetic diversity.
Full-text · Article · Jan 2013 · Microbiology and Immunology
[Show abstract][Hide abstract] ABSTRACT: In Japan, Mycobacterium sp. was isolated from the yellowtail, Seriola quinqueradiata, as a Mycobacterium marinum-like mycobacterium. The species was identified as M. marinum by a commercial mycobacterial DNA-DNA hybridization kit. Nevertheless, PCR restriction analysis of DNA of the RNA polymerase β-subunit gene definitively showed that Mycobacterium sp. is M. ulcerans. By PCR analysis, the genotypic characteristics of M. ulcerans were detected in Mycobacterium sp., although only the mup053 gene sequence was absent, as previously found in the other piscine mycobacteria such as M. marinum strains DL240490 and DL045, and M. pseudoshottsii. With one exception, Mycobacterium sp. and M. pseudoshottsii had identical 16S rRNA gene sequences, which was also probably true of M. marinum strains DL240490 and DL045. Similarly, by comparisons of the 16S rRNA gene, ITS region, and hsp65 gene sequences, Mycobacterium sp. was more closely related to M. pseudoshottsii than to M. ulcerans or M. marinum. A PCR product of approximately 2,000 bp was amplified from region of difference 9 in Mycobacterium sp. The nucleotide sequence revealed the insertion of IS2404 whose sequence was 1,366 bp long. In this region, novel single nucleotide polymorphisms were identified, which distinguished Mycobacterium sp. from M. marinum strain DL240490 and M. pseudoshottsii. Our findings raise the possibility that they have a common ancestor. Further studies are required to improve our understanding of the relationship between their geographical origin and genetic diversity.
Full-text · Article · Oct 2012 · Microbiology and Immunology
[Show abstract][Hide abstract] ABSTRACT: Background
Merkel cell polyomavirus (MCPyV) was identified originally in Merkel cell carcinoma (MCC), a rare form of human skin neuroendocrine carcinoma. Evidence of MCPyV existence in other forms of malignancy such as cutaneous squamous cell carcinomas (SCCs) is growing. Cervical cancers became the focus of our interest in searching for potentially MCPyV-related tumors because: (i) the major histological type of cervical cancer is the SCC; (ii) the uterine cervix is a common site of neuroendocrine carcinomas histologically similar to MCCs; and (iii) MCPyV might be transmitted during sexual interaction as demonstrated for human papillomavirus (HPV). In this study, we aimed to clarify the possible presence of MCPyV in cervical SCCs from Japanese patients. Cervical adenocarcinomas (ACs) were also studied.
Formalin-fixed paraffin-embedded tissue samples from 48 cervical SCCs and 16 cervical ACs were examined for the presence of the MCPyV genome by polymerase chain reaction (PCR) and sequencing analyses. PCR analysis revealed that 9/48 cervical SCCs (19%) and 4/16 cervical ACs (25%) were positive for MCPyV DNA. MCPyV-specific PCR products were sequenced to compare them with reference sequences. The nucleotide sequences in the MCPyV large T (LT)-sequenced region were the same among MCPyV-positive cervical SCCs and AC. Conversely, in the MCPyV viral protein 1 (VP1)-sequenced region, two cervical SCCs and three cervical ACs showed several nucleotide substitutions, of which three caused amino acid substitutions. These sequencing results suggested that three MCPyV variants of the VP1 were identified in our cases. Immunohistochemistry showed that the LT antigen was expressed in tumor cells in MCPyV-positive samples. Genotyping of human HPV in the MCPyV-positive samples revealed that infected HPVs were HPV types 16, 31 and 58 for SCCs and HPV types 16 and 18 for ACs.
This study provides the first observation that MCPyV coexists in a subset of HPV-associated cervical cancers from Japanese patients. The prevalence of MCPyV in these lesions was close to that observed in the cutaneous SCCs. Further worldwide epidemiological surveys are warranted to determine the possible association of MCPyV with pathogenesis of cervical cancers.
[Show abstract][Hide abstract] ABSTRACT: Chronic lymphocytic leukemia (CLL) is the rarest adult leukemia in Japan, whereas it is the most common leukemia in the Western world. Recent studies from the United States and Germany suggest a possible etiological association between Merkel cell polyomavirus (MCPyV) and CLL, although no data have been reported from Eastern countries. To increase the volume of relevant data, this study investigated the prevalence and DNA loads of MCPyV and human polyomavirus 9 (HPyV9), another lymphotropic polyomavirus, in Japanese CLL cases.
We found that 9/27 CLL cases (33.3 %) were positive for MCPyV using quantitative real-time polymerase chain reaction analysis. The viral DNA loads ranged from 0.000017 to 0.0012 copies per cell. All cases were negative for HPyV9. One MCPyV-positive CLL case was evaluated by mutational analysis of the large T (LT) gene, which indicated the presence of wild-type MCPyV without a nucleotide deletion. DNA sequence analysis of the entire small T (ST) gene and the partial LT gene revealed that a Japanese MCPyV isolate, designated CLL-JK, had two nucleotide gaps when compared with the reference sequence of the North American isolate MCC350.
This study provides the first evidence that MCPyV is present in a subset of Japanese CLL cases with low viral DNA loads. MCPyV and HPyV9 are unlikely to contribute directly to the development of CLL in the majority of Japanese cases. MCPyV isolated from the Japanese CLL cases may constitute an Asian group and its pathogenicity needs to be clarified in future studies.
Preview · Article · Jun 2012 · Journal of Hematology & Oncology
[Show abstract][Hide abstract] ABSTRACT: Epstein-Barr virus (EBV) genotypes can be distinguished based on gene sequence differences in EBV nuclear antigens 2, 3A, 3B, and 3C, and the BZLF1 promoter zone (Zp). EBV subtypes and BZLF1 Zp variants were examined in Japanese patients with infectious mononucleosis, chronic active EBV infection, and EBV-associated hemophagocytic lymphohistiocytosis. The results of EBV typing showed that samples of infectious mononucleosis, chronic active EBV infection, and EBV-associated hemophagocytic lymphohistiocytosis all belonged to EBV type 1. However, sequencing analysis of BZLF1 Zp found three polymorphic Zp variants in the same samples. The Zp-P prototype and the Zp-V3 variant were both detected in infectious mononucleosis and chronic active EBV infection. Furthermore, a novel variant previously identified in Chinese children with infectious mononucleosis, Zp-V1, was also found in 3 of 18 samples of infectious mononucleosis, where it coexisted with the Zp-P prototype. This is the first evidence that the EBV variant distribution in Japanese patients resembles that found in other Asian patients. The expression levels of 29 chronic active EBV infection-associated cellular genes were also compared in the three EBV-related disorders, using quantitative real-time reverse transcription polymerase chain reaction analysis. Two upregulated genes, RIPK2 and CDH9, were identified as common specific markers for chronic active EBV infection in both in vitro and in vivo studies. RIPK2 activates apoptosis and autophagy, and could be responsible for the pathogenesis of chronic active EBV infection.
No preview · Article · Jun 2012 · Journal of Medical Virology