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Find video protocols related to scientific articles indexed in Pubmed.
Two types of genetic carrier, the IncP genomic island and the novel IncP-1? plasmid, for the aac(2')-IIa gene that confers kasugamycin resistance in Acidovorax avenae ssp. avenae.
Mol. Plant Pathol.
PUBLISHED: 08-18-2014
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A unique aminoglycoside antibiotic, kasugamycin (KSM), has been used to control many plant bacterial and fungal diseases in several countries. The emergence of KSM-resistant Acidovorax avenae ssp. avenae and Burkholderia glumae, which cause rice bacterial brown stripe and rice bacterial grain and seedling rot, respectively, is a serious threat for the effective control of these diseases. Previously, we have identified the aac(2')-IIa gene, encoding a KSM 2'-N-acetyltransferase, from both KSM-resistant pathogens. Although all KSM-resistant isolates from both species possess the aac(2')-IIa gene, only A.?avenae strain 83 showed higher resistance than other strains. In this research, kinetic analysis indicates that an amino acid substitution from serine to threonine at position 146 of AAC(2')-IIa in strain 83 is not involved in this increased resistance. Whole draft genome analysis of A.?avenae 83 shows that the aac(2')-IIa gene is carried by the novel IncP-1? plasmid pAAA83, whereas the genetic carrier of other strains, the IncP genomic island, is inserted into their chromosomes. The difference in the nucleotides of the promoter region of aac(2')-IIa between strain 83 and other strains indicates an additional transcription start site and results in the increased transcription of aac(2')-IIa in strain 83. Moreover, biological characterization of pAAA83 demonstrates that it can be transferred by conjugation and maintained in the host cells. These results demonstrate that acquisition of the aac(2')-IIa gene takes place in at least two ways and that the gene module, which includes aac(2')-IIa and the downstream gene, may be an important unit for the dissemination of antibiotic resistance.
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Detection of a pneumonia virus of mice (PVM) in an African hedgehog (Atelerix arbiventris) with suspected wobbly hedgehog syndrome (WHS).
Vet. Microbiol.
PUBLISHED: 07-29-2014
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A pneumonia virus of mice (PVM) from an African hedgehog (Atelerix arbiventris) with suspected wobbly hedgehog syndrome (WHS) was detected and genetically characterized. The affected hedgehog had a nonsuppurative encephalitis with vacuolization of the white matter, and the brain samples yielded RNA reads highly homogeneous to PVM strain 15 (96.5% of full genomic sequence homology by analysis of next generation sequencing). PVM antigen was also detected in the brain and the lungs immunohistochemically. A PVM was strongly suggested as a causative agent of encephalitis of a hedgehog with suspected WHS. This is a first report of PVM infection in hedgehogs.
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Detection of enterovirus genome sequence from diarrheal feces of goat.
Virus Genes
PUBLISHED: 03-07-2014
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Goat diarrheal feces were subjected to metagenome analysis by the next-generation sequencing. Nucleotide sequences with homology to enteroviruses were obtained. Primers for RT-PCR were designed based on the nucleotide sequence of these sequences at the 5'-untranslated region, and we determined 563 bp nucleotide sequences that showed homology to bovine-like and ovine enteroviruses (77-87 %). We named the virus detected in this study goat enterovirus G1 (GEV-G1). In the phylogenetic analysis, GEV-G1 belonged to a cluster containing ovine enteroviruses. To our knowledge, this is the first report on nucleotide sequences of an enterovirus infecting Japanese goats.
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Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer.
Vet. Microbiol.
PUBLISHED: 03-03-2014
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There are few reports describing diarrhea of adult cattle caused by group A rotaviruses. Here, we report the identification of a novel bovine group A rotavirus from diarrhea of adult cows. A group A rotavirus was detected from an epizootic outbreak of diarrhea in adult cows with a decrease in milk production in Japan in 2013. The comprehensive genomic analyses from fecal samples by viral metagenomics using a next-generation sequencer revealed that it had an unreported genotype combination G15P[14]. The genome constellation of this strain, namely, RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] was G15-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 representing VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5, respectively. Each gene segment of Tottori-SG was most closely related to Japanese bovine group A rotaviruses suggesting that Tottori-SG might have derived from multiple reassortment events from group A rotavirus strains circulating among Japanese cattle. No other diarrhea pathogen of adult cattle was detected by routine diagnosis and metagenomics. Viral metagenomics, using a next-generation sequencer, is useful to characterize group A rotaviruses from fecal samples and offers unbiased comprehensive investigations of pathogen.
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Demonstration of marmosets (Callithrix jacchus) as a non-human primate model for secondary dengue virus infection: high levels of viraemia and serotype cross-reactive antibody responses consistent with secondary infection of humans.
J. Gen. Virol.
PUBLISHED: 12-09-2013
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There are four dengue virus (DENV) serotypes. Primary infection with one does not confer protective immunity against the others. We have previously reported that the marmoset (Callithrix jacchus) is a useful primary DENV infection model. It has been reported that secondary DENV infection with a heterotypic serotype induces viremia kinetics and antibody responses that differ from those in primary infection. Thus, it is important to determine the utility of the marmoset as a model for secondary DENV infection. Marmosets were infected with heterologous DENV in secondary inoculation and, viremia kinetics and antibody responses were analyzed. Marmosets consistently developed high levels of viremia after secondary inoculation with heterologous DENV serotypes. IgM responses were lower as compared to primary inoculation, while IgG responses were rapid and, high levels of IgG was induced. Serotype cross-reactive neutralizing activities were detected as early as 4 days after inoculation. In addition, viremia titers were higher when assayed with Fc?R-expressing BHK cells, than when assayed with conventional Fc?R-negative BHK cells, suggesting the presence of infectious virus-antibody immune complex. After secondary infection with heterotypic DENV, marmosets demonstrated viremia kinetics, IgM and IgG responses, and high levels of serotype cross-reactive neutralizing antibody responses, all of which were consistent with secondary DENV infection in humans. The results indicate the marmoset to be a useful animal for studying secondary, as well as primary, DENV infection.
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The First Identification and Retrospective Study of Severe Fever With Thrombocytopenia Syndrome in Japan.
J. Infect. Dis.
PUBLISHED: 11-14-2013
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Background.?Severe fever with thrombocytopenia syndrome (SFTS) is caused by SFTS virus (SFTSV), a novel bunyavirus reported to be endemic in central and northeastern China. This article describes the first identified patient with SFTS and a retrospective study on SFTS in Japan.Methods.?Virologic and pathologic examinations were performed on the patients samples. Laboratory diagnosis of SFTS was made by isolation/genome amplification and/or the detection of anti-SFTSV immunoglobulin G antibody in sera. Physicians were alerted to the initial diagnosis and asked whether they had previously treated patients with symptoms similar to those of SFTS.Results.?A female patient who died in 2012 received a diagnosis of SFTS. Ten additional patients with SFTS were then retrospectively identified. All patients were aged ?50 years and lived in western Japan. Six cases were fatal. The ratio of males to females was 8:3. SFTSV was isolated from 8 patients. Phylogenetic analyses indicated that all of the Japanese SFTSV isolates formed a genotype independent to those from China. Most patients showed symptoms due to hemorrhage, possibly because of disseminated intravascular coagulation and/or hemophagocytosis.Conclusions.?SFTS has been endemic to Japan, and SFTSV has been circulating naturally within the country.
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Detection of Bovine Group A Rotavirus Using Rapid Antigen Detection Kits, RT-PCR and Next-Generation DNA Sequencing.
J. Vet. Med. Sci.
PUBLISHED: 08-02-2013
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We investigated the sensitivity of human rotavirus rapid antigen detection (RAD) kits, RT-PCR and next-generation DNA sequencing (NGS) for detection of bovine group A rotavirus (RVA). The Dipstick Eiken Rota (Dipstick) showed the highest sensitivity out of the seven RAD kits against all selected strains in limited dilution analyses, which was consistent with the results of equine rotavirus previously reported. RT-PCR had 10(0)-10(3)-fold higher sensitivity than the Dipstick. The NGS using RT-PCR negative thirteen fecal samples revealed that all samples yielded RVA reads and especially two of them covered all 11 genome segments. Moreover, mapping reads to reference sequences allowed genotyping. The NGS would be sensitive and useful for analysis of less dependent on specific primers and screening presumption of genotype.
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Existence of feline morbillivirus infection in Japanese cat populations.
Arch. Virol.
PUBLISHED: 06-07-2013
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Feline morbillivirus (FmoPV) is a member of a new virus species that has only been found in the Hong Kong cat population. For the first time, however, we have now detected nucleotide sequences similar to FmoPV in samples from Japanese cat populations. The positive rates for urine and blood samples from Japanese cats were 6.1 % (5/82) and 10 % (1/10), respectively. These sequences are similar to the previously reported FmoPV, with 92-94 % identity, and substantially different from all other morbilliviruses. Phylogenetic analysis of the identified Japanese FmoPVs and other morbilliviruses demonstrated a pattern similar to those previously published for the FmoPV viruses isolated in Hong Kong. FmoPV RNA was also detected from formalin-fixed paraffin-embedded (FFPE) kidney tissues of cats with nephritis, with a positive rate of 40 % (4/10). By using nested-set primers based on the FmoPV sequence and RNA from FFPE tissues, we demonstrated the existence of FmoPV infection in Japanese cats and established the method for detection of the FmoPV RNA from kidney tissues prepared for pathology examinations, which is useful for studies on the pathogenicity of the virus.
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Molecular epidemiology of avian bornavirus from pet birds in Japan.
Virus Genes
PUBLISHED: 04-04-2013
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Recently, Avian bornavirus (ABV) was detected in proventricular dilatation disease (PDD) affected-birds and feather picking diseases affected-birds. However, the pathogenicity of ABV has not been thoroughly investigated. In this study, we surveyed ABV in pet birds in Japan. We found four ABV-infected birds among 93 pet birds using RT-PCR, and genotypes of the ABV were determined as ABV-2 and -4. Two of the birds positive for ABV-4 showed proventricular dilatation typically found in PDD, and chronic stomach disturbance, whereas two of the birds positive for ABV-2 showed unexplained behavioral problems that are tapping, autophagia, and cloaca prolapse.
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Detection of dengue virus nonstructural protein 1 (NS1) by using ELISA as a useful laboratory diagnostic method for dengue virus infection of international travelers.
J Travel Med
PUBLISHED: 03-08-2013
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Dengue virus ( DENV) nonstructural protein 1 ( NS1) has been used as a novel diagnostic marker during the early phase of DENV infection.
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Dynamics of cellular immune responses in the acute phase of dengue virus infection.
Arch. Virol.
PUBLISHED: 02-05-2013
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In this study, we examined the dynamics of cellular immune responses in the acute phase of dengue virus (DENV) infection in a marmoset model. Here, we found that DENV infection in marmosets greatly induced responses of CD4/CD8 central memory T and NKT cells. Interestingly, the strength of the immune response was greater in animals infected with a dengue fever strain than in those infected with a dengue hemorrhagic fever strain of DENV. In contrast, when animals were re-challenged with the same DENV strain used for primary infection, the neutralizing antibody induced appeared to play a critical role in sterilizing inhibition against viral replication, resulting in strong but delayed responses of CD4/CD8 central memory T and NKT cells. The results in this study may help to better understand the dynamics of cellular and humoral immune responses in the control of DENV infection.
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CD16(+) natural killer cells play a limited role against primary dengue virus infection in tamarins.
Arch. Virol.
PUBLISHED: 07-29-2011
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CD16 is a major molecule expressed on NK cells. To directly assess the role of natural killer (NK) cells in dengue virus (DENV) infection in vivo, CD16 antibody-treated tamarins were inoculated with a DENV-2 strain. This resulted in the transient depletion of CD16(+) NK cells, whereas no significant effects on the overall levels or kinetics of plasma viral loads and antiviral antibodies were observed in the treated monkeys when compared to control monkeys. It remains elusive whether the CD16(-) NK subpopulation could play an important role in the control of primary DENV infection.
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Common marmoset (Callithrix jacchus) as a primate model of dengue virus infection: development of high levels of viraemia and demonstration of protective immunity.
J. Gen. Virol.
PUBLISHED: 06-22-2011
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Dengue virus (DENV) causes a wide range of illnesses in humans: dengue fever (DF), dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Animal models that constantly develop high levels of viraemia are required for the development of protective and preventive measures. Common marmosets (Callithrix jacchus) demonstrated high levels of viraemia after inoculation with clinical isolates of four serotypes of DENV; in particular, over 10(6) genome copies ml(-1) after inoculation with DENV-2. Non-structural protein 1 and DENV-specific IgM and IgG antibodies were consistently detected. The DENV-2 genome was detected in lymphoid organs including the lymph nodes, spleen and thymus, and also in non-lymphoid organs. DENV antigen was detected by immunohistochemistry in the liver and spleen from inoculated marmosets. Four marmosets were reinoculated with DENV-2 at 33 weeks after primary inoculation with DENV-2. The DENV-2 genome was not detected in any of these marmosets, indicating protection from a secondary infection. The results indicate that common marmosets are highly sensitive to DENV infection, and suggest that marmosets could be a reliable primate model for the evaluation of candidate vaccines.
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Bat coronaviruses and experimental infection of bats, the Philippines.
Emerging Infect. Dis.
PUBLISHED: 08-04-2010
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Fifty-two bats captured during July 2008 in the Philippines were tested by reverse transcription-PCR to detect bat coronavirus (CoV) RNA. The overall prevalence of virus RNA was 55.8%. We found 2 groups of sequences that belonged to group 1 (genus Alphacoronavirus) and group 2 (genus Betacoronavirus) CoVs. Phylogenetic analysis of the RNA-dependent RNA polymerase gene showed that groups 1 and 2 CoVs were similar to Bat-CoV/China/A515/2005 (95% nt sequence identity) and Bat-CoV/HKU9-1/China/2007 (83% identity), respectively. To propagate group 2 CoVs obtained from a lesser dog-faced fruit bat (Cynopterus brachyotis), we administered intestine samples orally to Leschenault rousette bats (Rousettus leschenaulti) maintained in our laboratory. After virus replication in the bats was confirmed, an additional passage of the virus was made in Leschenault rousette bats, and bat pathogenesis was investigated. Fruit bats infected with virus did not show clinical signs of infection.
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Molecular cloning and expression analysis of bat toll-like receptors 3, 7 and 9.
J. Vet. Med. Sci.
PUBLISHED: 11-25-2009
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In this study, cDNA of Toll-like receptors (TLR) 3, 7 and 9 were synthesized and completely sequenced. The coding regions of cDNA for bat TLR3, TLR7 and TLR9 were 2,718, 3,150 and 3,090 bp in length, respectively. The open reading frames encoded 905, 1,049 and 1,029 amino acids for TLR3, TLR7 and TLR9, respectively. The nucleotide sequences, predicted amino acid sequences and predicted domain structures of the three bat TLRs had high homology with those of other mammals. In addition, the expression profiles of each TLR in main organs were analyzed. Expression of TLR3 was highest in the liver, whereas the expressions of TLR7 and TLR9 were highest in the spleen.
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Molecular cloning and sequencing of the cDNAs encoding the bat interleukin (IL)-2, IL-4, IL-6, IL-10, IL-12p40, and tumor necrosis factor-alpha.
J. Vet. Med. Sci.
PUBLISHED: 11-17-2009
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This is the first report on the cDNA sequences of bat interleukin (IL)-2, IL-4, IL-6, IL-10, IL-12 p40, and tumor necrosis factor (TNF)-alpha. The cDNAs of bat IL-2, IL-4, IL-6, IL-10, IL-12 p40, and TNF-alpha comprise 459, 405, 624, 537, 990, and 699 base pairs respectively. Moreover, each of the cDNAs of bat IL-2, IL-4, IL-6, IL-10, IL-12 p40, and TNF-alpha contain a single open reading frames encoding 152, 134, 207, 178, 329, and 232 amino acids, respectively. The comparison of bat cytokines with Perrissodactyla (horse), Carnivora (dog and cat), and Cetartiodactyla (cattle and pig) orthologs revealed a high degree of homology. Although the N-terminal amino acids and cysteine residues are highly conserved in each mature cytokine, the deduced N-linked glycosylation sites vary across species.
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Direct experimental occlusion of the distal middle cerebral artery induces high reproducibility of brain ischemia in mice.
Exp. Anim.
PUBLISHED: 01-20-2009
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Several investigators have used murine models to investigate the pathophysiology of brain ischemia. The focal ischemic model is a closer approximation to human stroke which includes a necrotic core, penumbra, and undamaged tissue. Occlusion of a unilateral artery, especially the middle cerebral artery (MCA), is performed in this model, but collateral circulation often induces variation of ischemic lesions both qualitatively and quantitatively. It is likely that the more proximal the artery which is unilaterally occluded is, the more inconsistent the outcomes. The present study was designed to examine the reproducibility of infarct lesion by distal or proximal artery occlusion. Direct occlusion of the distal MCA was performed and compared with unilateral common carotid artery occlusion (CCAO) in C57BL/6 mice. Direct MCA occlusion (MCAO) consistently induced ischemic lesions in cortical areas. All model animals (n=14) survived 24 h after occlusion, and exhibited a maximum infarct volume (20.0 +/- 5.0%). In contrast, permanent and transient unilateral CCAO models had mortality rates of 62.5 and 25.0%, and showed severe to absent lesions with the infarct volumes of 29.0 +/- 20.8 and 33.2 +/- 24.2%, respectively. In conclusion, distal MCAO produces high reproducibility of ischemic insults and survivability compared to unilateral CCAO. Thus, distal MCAO is a useful method for the focal ischemic model.
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Changes in hematological and serum biochemical parameters in common marmosets (Callithrix jacchus) after inoculation with dengue virus.
J. Med. Primatol.
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Marmosets are susceptible to dengue virus (DENV) infection. However, blood parameter data and clinical signs of DENV-infected marmosets are limited.
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Detection of dengue virus genome in urine by real-time reverse transcriptase PCR: a laboratory diagnostic method useful after disappearance of the genome in serum.
J. Clin. Microbiol.
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The reemergence of dengue virus (DENV) infection has created a requirement for improved laboratory diagnostic procedures. In this study, DENV genome detection in urine was evaluated as a diagnostic method. The DENV genome was detected by real-time reverse transcriptase PCR (RT-PCR) in urine and serum of dengue patients. The detection rate of DENV genome in urine was 25% (2/8) on disease days 0 to 3 and 32% (7/22) on days 4 to 5. The rate was 50% or higher on days 6 to 16, 52% (11/21) on days 6 to 7, 78% (7/9) on days 8 to 9, 80% (4/5) on days 10 to 11, 50% (2/4) on days 12 to 13, and 60% (3/5) on days 14 to 16. The last positive urine sample was on day 16. The detection rates in serum were highest on days 0 to 3 and were greater than 50% on days 0 to 7. Detection rates decreased thereafter, and the last positive detection was on day 11. These results indicate that the time frames for positive detection differ between urine and serum samples, whereby detection rates of 50% or higher are evident between days 6 to 16 for urine samples and days 0 to 7 for serum samples. Nucleotide sequences of PCR products were identical between urine and serum samples. The detection of DENV genome in urine samples by real-time RT-PCR is useful to confirm DENV infection, particularly after viremia disappears.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.