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1.
Mycobiology ; 49(2): 122-132, 2021.
Article in English | MEDLINE | ID: mdl-37970183

ABSTRACT

The reexamination of the fungal genus Botryosphaeria on 12 plant species of 10 families was carried out based on molecular phylogenetic analyses using the regions of translation elongation factor 1-α, ß-tubulin, DNA-directed RNA polymerase II subunit, and internal transcribed spacer region of rDNA and morphological characteristics. Japanese isolates were divided into five clades and include Botryosphaeria dothidea, B. qingyuanensis, B. sinensis, and Botryosphaeria spp. Two species, B. qingyuanensis and B. sinensis have been newly added to the Japanese mycoflora, but their host plants are not specified. Botryosphaeria tenuispora isolated from Leucothoe fontanesiana and insect galls on fruits of Aucuba japonica has been proposed as a new species.

2.
Virus Genes ; 54(1): 149-154, 2018 Feb.
Article in English | MEDLINE | ID: mdl-28986679

ABSTRACT

Pyrus pyrifolia cryptic virus (PpCV) had been previously reported from Japanese pear (Pyrus pyrifolia). In analyses of Japanese pear, two other double-stranded (ds) RNA molecules (dsRNA4 and 5) were observed along with the three dsRNA segments from PpCV on an electrophoretic profile of isolated dsRNA. When the purified dsRNA sample was deep sequenced by a next-generation sequencer, two de novo assembled contigs corresponding to dsRNA4 and 5, with predicted amino acid sequences showing homologies to the RNA-dependent RNA polymerase and the capsid protein of Rose partitivirus, respectively, were found by BLAST analysis. The relationships between the two contigs and dsRNA4, 5 were confirmed by northern blot analyses with probes amplified using primers designed from the contigs. Terminal sequence analyses by rapid amplification of cDNA ends revealed that dsRNA4 and 5 were 1945 and 1788 bp long, respectively. The 5' terminal sequences (GUCAAAUU) of dsRNA4 and 5 were conserved. Based on genome size and phylogenetic analyses, the newly found virus is thought to be a member of the genus Alphapartitivirus. Thus, it has been designated as Pyrus pyrifolia partitivirus 2.


Subject(s)
Plant Viruses/classification , Plant Viruses/isolation & purification , Pyrus/virology , RNA Viruses/classification , RNA Viruses/isolation & purification , Blotting, Northern , Conserved Sequence , High-Throughput Nucleotide Sequencing , Japan , Phylogeny , Plant Viruses/genetics , RNA Viruses/genetics , RNA-Dependent RNA Polymerase/genetics , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Viral Proteins/genetics
3.
Virus Res ; 240: 64-68, 2017 08 15.
Article in English | MEDLINE | ID: mdl-28760347

ABSTRACT

According to previous studies, three double-stranded (ds) RNA molecules (dsRNA1, 2, and 3) detected in Japanese pear are transmitted to the next generation with high frequency through both ovules and pollen. Nucleotide sequence analysis of dsRNA1-encoding RNA-dependent RNA polymerase (RdRp) has suggested that these dsRNAs are related to a cryptovirus named Pyrus pyrifolia cryptic virus (PpCV). In this study, purified dsRNA prepared from a PpCV-infected Japanese pear cultivar was subjected to next-generation deep sequencing. This sequencing generated two de novo assembled contigs corresponding to dsRNA2 and 3, with BLAST analysis of the predicted amino acid sequences indicating homology to capsid proteins (CPs) of the cryptoviruses persimmon cryptic virus and Sinapis alba cryptic virus 1, respectively. Relationships between the two contigs and dsRNA2 and 3 were confirmed by northern blot hybridization with probes generated using primers designed from the assembled contigs. Rapid amplification of cDNA ends analyses of 5'- and 3'-terminal sequences of dsRNA2 and 3 revealed that these two dsRNAs consist of 1523 and 1481bp, respectively. The 5'-terminal sequences (AGAAUUUC) of dsRNA1, 2 and 3 were found to be conserved. Phylogenetic analysis of deduced amino acid sequences of the two CP-like variants indicated that PpCV belongs to Deltapartitivirus (Partitiviridae). Our results imply that PpCV is tri-segmented.


Subject(s)
Capsid Proteins/genetics , Genome, Viral , Plant Diseases/virology , Pyrus/virology , RNA Viruses/isolation & purification , Capsid Proteins/metabolism , High-Throughput Nucleotide Sequencing , Phylogeny , RNA Viruses/classification , RNA Viruses/genetics , RNA, Viral/genetics , RNA, Viral/metabolism
4.
Virus Genes ; 52(6): 835-847, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27550368

ABSTRACT

Many bands were detected on an electrophoretic profile of double-stranded (ds) RNA preparation from a single strain of Fusarium poae isolated from wheat. When the purified dsRNA sample was deep-sequenced by a next-generation sequencer, sixteen virus-like assembled contigs with predicted amino acid sequences showing homologies to respective viral RNA-dependent RNA polymerases (RdRps) were found by BLAST analysis. Fourteen out of sixteen sequences showed homologies to RdRps of known mycoviruses, that is, four mitoviruses, two narnaviruses, two partitiviruses, an alternavirus, a fusarivirus, a hypovirus, a victorivirus, and two unclassified mycoviruses, Sclerotinia sclerotiorum dsRNA mycovirus-L and Aspergillus foetidus slow virus 2, respectively. The other two putative viral RdRp sequences showed homologies to those of members of negative-stranded RNA viruses, the Ophiovirus and the Phlebovirus respectively, which mycoviruses had been not ever assigned to. Based on genome structure and phylogenetic analysis, both viruses were thought to be members of novel respective negative-stranded RNA virus groups. The presences of all sixteen viral RdRp sequences identified by BLAST analysis were confirmed by sequencing RT-PCR products generated from the starting dsRNA material using primers designed from the de novo assembled sequences of respective putative mycoviruses. Since the single strain of F. poae was considered to be multiply infected with mycoviruses from novel taxonomical groups in addition to many common mycoviruses, the RNA virome of the strain was found to be highly diverse.


Subject(s)
Fusarium/virology , High-Throughput Nucleotide Sequencing , RNA Viruses/genetics , Computational Biology , Fungal Viruses/classification , Fungal Viruses/genetics , Genome, Viral , Phylogeny , RNA Viruses/classification , RNA, Double-Stranded , RNA, Viral , Sequence Analysis, DNA , Triticum/microbiology
5.
Virus Res ; 219: 73-82, 2016 07 02.
Article in English | MEDLINE | ID: mdl-26718720

ABSTRACT

A new virus termed Rosellinia necatrix megabirnavirus 2 (RnMBV2) was molecularly and biologically characterized. RnMBV2 was originally harbored in isolate W8 of R. necatrix co-infected with the previously reported virus Rosellinia necatrix partitivirus 1 (RnPV1). RnMBV2 has molecular features similar and different from precedent megabirnaviruses, Rosellinia necatrix megabirnavirus 1 (RnMBV1) and Sclerotinia sclerotiorum megabirnavirus 1 (SsMBV1). The two genomic segments of RnMBV2 (9.0-kbp dsRNA1 and 8.0-kbp dsRNA2) each possess two open reading frames (ORF1 and 2 on dsRNA1 and ORF3 and 4 on dsRNA2), with a well conserved 5'-long untranslated region (UTR) of 1.7-1.8kb between the segments, and relatively short 3'-UTR. The RnMBV2 dsRNA1-coded capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) show higher sequence identity to those of SsMBV1 than to those of RnMBV1, whereas the RnMBV2 ORF3-coded protein is more closely related to the counterpart of RnMBV1. No significant amino acid sequence similarity was detected among ORF4-coded sequences of the three megabirnaviruses. Virion transfection and co-culturing allowed for single and double infection of mycelial incompatible isolates W37 and W97 by RnMBV2 and/or RnPV1. Their comparative analyses showed RnMBV2 to be able to confer hypovirulence with the aid of a co-infecting RnPV1, while the individual viruses exhibited asymptomatic infections. Interestingly, RnPV1 accumulation appeared to be increased in co-infected fungal strain with two segments of RnMBV2 relative to singly infected fungal strains. Furthermore, the dispensability of RnMBV2 dsRNA2 was demonstrated to be similar to that of the other two megabirnaviruses.


Subject(s)
Ascomycota/virology , Coinfection , Fungal Viruses/classification , Fungal Viruses/physiology , Host-Pathogen Interactions , Phylogeny , RNA, Viral , Symbiosis , Virulence
6.
Virus Genes ; 50(3): 466-73, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25687123

ABSTRACT

The filamentous fungus Fusarium spp. includes several important plant pathogens. We attempted to reveal presence of double-stranded (ds) RNAs in the genus. Thirty-seven Fusarium spp. at the MAFF collection were analyzed. In the strains of Fusarium coeruleum, Fusarium globosum and Fusarium solani f. sp. pisi, single dsRNA bands were detected. The strains of F. coeruleum and F. solani f. sp. pisi cause potato dry rot and mulberry twig blight, respectively. Sequence analyses revealed that dsRNAs in F. coeruleum and F. globosum consisted of 2423 and 2414 bp, respectively. Using the fungal mitochondrial translation table, the positive strands of these cDNAs were found to contain single open reading frames with the potential to encode a protein of putative 757 and 717 amino acids (molecular mass 88.5 and 84.0 kDa, respectively), similar to RNA-dependent RNA polymerases of members of the genus Mitovirus. These dsRNAs in F. coeruleum and F. globosum were assigned to the genus Mitovirus (family Narnaviridae), and these two mitoviruses were designated as Fusarium coeruleum mitovirus 1 and Fusarium globosum mitovirus 1. On the other hand, a positive strand of cDNA (1950 bp) from dsRNA in F. solani f. sp. pisi contained an ORF potentially encoding a putative RdRp of 608 amino acids (72.0 kDa). The putative RdRp was shown to be related to those of members of the genus of Alphapartitivirus (family Partitiviridae). We coined the name Fusarium solani partitivirus 2 for dsRNA in F. solani f. sp. pisi.


Subject(s)
Fusarium/virology , RNA Viruses/genetics , RNA Viruses/isolation & purification , RNA, Double-Stranded/genetics , RNA, Viral/genetics , Cluster Analysis , Fusarium/isolation & purification , Models, Molecular , Molecular Sequence Data , Nucleic Acid Conformation , Open Reading Frames , Plant Diseases/microbiology , Sequence Analysis, DNA , Sequence Homology
7.
Virology ; 450-451: 308-15, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24503094

ABSTRACT

Rosellinia necatrix megabirnavirus 1 (RnMBV1) is a bi-segmented double-stranded RNA mycovirus that reduces the virulence of the fungal plant pathogen R. necatrix. We isolated strains of RnMBV1 with genome rearrangements (RnMBV1-RS1) that retained dsRNA1, encoding capsid protein (ORF1) and RNA-dependent RNA polymerase (ORF2), and had a newly emerged segment named dsRNAS1, but with loss of dsRNA2, which contains two ORFs of unknown function. Analyses of two variants of dsRNAS1 revealed that they both originated from dsRNA1 by deletion of ORF1 and partial tandem duplication of ORF2, retaining a much shorter 5' untranslated region (UTR). R. necatrix transfected with RnMBV-RS1 virions showed maintenance of virulence on host plants compared with infection with RnMBV1. This suggests that dsRNAS1 is able to be transcribed and packaged, as well as suggesting that dsRNA2, while dispensable for virus replication, is required to reduce the virulence of R. necatrix.


Subject(s)
Genome, Viral , Malus/microbiology , Plant Diseases/microbiology , RNA Viruses/genetics , Recombination, Genetic , Xylariales/pathogenicity , Xylariales/virology , RNA Viruses/classification , RNA Viruses/physiology , Virulence , Virus Replication , Xylariales/physiology
8.
Appl Environ Microbiol ; 79(12): 3684-91, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23563943

ABSTRACT

Heterogenic incompatibility is considered a defense mechanism against deleterious intruders such as mycovirus. Rosellinia necatrix shows strong heterogenic incompatibility. In the heterogenic incompatibility reaction, the approaching hyphae hardly anastomosed, a distinctive barrage line formed, and green fluorescent protein (GFP)-labeled hyphae quickly lost their fluorescence when encountering incompatible hyphae. In this study, transmission of a hypovirulence-conferring mycovirus to strains with different genetic backgrounds was attempted. Various chemical reagents considered to affect the programmed cell death pathway or cell wall modification were examined. Treatment with zinc compounds was shown to aid in transmission of mycoviruses to strains with different genetic backgrounds. In incompatible pairings, treatment with zinc compounds accelerated hyphal anastomosis; moreover, cytosolic GFP was transmitted to the newly joined hyphae. These results suggest that zinc compounds not only increase hyphal anastomosis but also attenuate heterogenic incompatibility.


Subject(s)
Gene Transfer Techniques , Hyphae/physiology , RNA Viruses/physiology , Virus Internalization/drug effects , Xylariales/virology , Zinc Compounds/pharmacology , DNA Primers/genetics , Hyphae/drug effects , Microscopy, Electron, Transmission , Microscopy, Fluorescence , RNA Viruses/isolation & purification , Xylariales/ultrastructure
9.
FEMS Microbiol Ecol ; 83(1): 49-62, 2013 Jan.
Article in English | MEDLINE | ID: mdl-22808916

ABSTRACT

In general, mycoviruses are transmitted through hyphal anastomosis between vegetatively compatible strains of the same fungi, and their entire intracellular life cycle within host fungi limits transmission to separate species and even to incompatible strains belonging to the same species. Based on field observations of the white root rot fungus, Rosellinia necatrix, we found two interesting phenomena concerning mycovirus epidemiology. Specifically, apple trees in an orchard were inoculated with one or two R. necatrix strains that belonged to different mycelial compatibility groups (MCGs), strains W563 (virus-free, MCG139) and NW10 (carrying a mycovirus-like double-stranded (ds) RNA element (N10), MCG442). Forty-two sub-isolates of R. necatrix, which were retrieved 2-3 years later, were all genetically identical to W563 or NW10: however, 22 of the sub-isolates contained novel dsRNAs. Six novel dsRNAs (S1-S6) were isolated: S1 was a new victorivirus; S2, S3, and S4 were new partitiviruses; and S5 and S6 were novel viruses that could not be assigned to any known mycovirus family. N10 dsRNA was detected in three W563 sub-isolates. These findings indicated that novel mycoviruses, from an unknown source, were infecting strains W563 and NW10 of R. necatrix in the soil, and that N10 dsRNA was being transmitted between incompatible strains, NW10 to W563.


Subject(s)
RNA Viruses/isolation & purification , RNA, Double-Stranded/isolation & purification , RNA, Viral/isolation & purification , Soil Microbiology , Xylariales/virology , Amplified Fragment Length Polymorphism Analysis , Gene Library , Genotype , Malus/microbiology , Plant Roots/microbiology , RNA Viruses/classification , RNA Viruses/genetics , Xylariales/genetics
10.
Virology ; 426(1): 42-50, 2012 Apr 25.
Article in English | MEDLINE | ID: mdl-22321722

ABSTRACT

Here we report the biological and molecular attributes of a novel dsRNA virus isolated from Rosellinia necatrix, a filamentous phytopathogenic fungus. The virus, termed Rosellinia necatrix quadrivirus 1 (RnQV1), forms rigid spherical particles approximately 45 nm in diameter in infected mycelia. The particles contain 4 dsRNA segments, dsRNA1 to dsRNA4, with a size range of 4.9 to 3.7 kbp, each possessing a single large ORF. A comparison of the virus-infected and -cured isogenic fungal strains suggested that RnQV1 infection has no appreciable phenotypic effects. Phylogenetic analysis using the dsRNA3-encoded RdRp sequence revealed that RnQV1 is more distantly related to quadripartite chrysoviruses than to monopartite totiviruses, and is placed in a distinct group from other mycoviruses. No significant sequence similarities were evident between known proteins and RnQV1 structural proteins shown to be encoded by dsRNA2 or dsRNA4. These suggest that RnQV1 is a novel latent virus, belonging to a new family.


Subject(s)
Plant Diseases/microbiology , RNA Viruses/isolation & purification , Xylariales/virology , Amino Acid Sequence , Base Sequence , Molecular Sequence Data , Phylogeny , Pyrus/microbiology , RNA Viruses/chemistry , RNA Viruses/classification , RNA Viruses/genetics , Sequence Alignment , Viral Proteins/chemistry , Viral Proteins/genetics , Xylariales/isolation & purification , Xylariales/physiology
11.
Phytopathology ; 100(9): 922-30, 2010 Sep.
Article in English | MEDLINE | ID: mdl-20701490

ABSTRACT

The potential host range of mycoviruses is poorly understood because of the lack of suitable inoculation methods. Recently, successful transfection has been reported for somatically incompatible fungal isolates with purified virus particles of two mycoviruses, the partitivirus RnPV1-W8 (RnPV1) and the mycoreovirus RnMyRV3/W370 (MyRV3), from the white root rot fungus Rosellinia necatrix (class Sordariomycetes, subclass Xylariomycetidae). These studies examined and revealed the effect of the mycoviruses on growth and pathogenicity of R. necatrix. Here, we extended the experimental host range of these two mycoviruses using a transfection approach. Protoplasts of other phytopathogenic Sordariomycetous fungi-Diaporthe sp., Cryphonectria parasitica, Valsa ceratosperma (Sordariomycetidae), and Glomerella cingulata (Hypocreomycetidae)-were inoculated with RnPV1 and MyRV3 viral particles. The presence of double-stranded RNA viral genomes in regenerated mycelia of Diaporthe sp., C. parasitica, and V. ceratosperma confirmed both types of viral infections in these three novel host species. An established RnPV1 infection was confirmed in G. cingulata but MyRV3 did not infect this host. Horizontal transmission of both viruses from newly infected strains to virus-free, wild-type strains through hyphal anastomosis was readily achieved by dual culture; however, vertical transmission through conidia was rarely observed. The virulence of Diaporthe sp., C. parasitica, and V. ceratosperma strains harboring MyRV3 was reduced compared with their virus-free counterpart. In summary, our protoplast inoculation method extended the experimental host range of RnPV1-W8 and MyRV3 within the class Sordariomycetes and revealed that MyRV3 confers hypovirulence to the new hosts, as it does to R. necatrix.


Subject(s)
Ascomycota/virology , Protoplasts/virology , Reoviridae/physiology , Host-Pathogen Interactions , Reoviridae/pathogenicity , Transfection , Virulence
12.
Nat Protoc ; 5(6): 1051-60, 2010 Jun.
Article in English | MEDLINE | ID: mdl-20539281

ABSTRACT

The cell is a crowded environment in which proteins interact specifically with other proteins, nucleic acids, cofactors and ligands. Atomic resolution structural explanation of proteins functioning in this environment is a main goal of biochemical research. Recent improvements to nuclear magnetic resonance (NMR) hardware and methodology allow the measurement of high-resolution heteronuclear multidimensional NMR spectra of macromolecules in living cells (in-cell NMR). In this study, we describe a protocol for the stable isotope ((13)C, (15)N and (2)H) labeling and structure determination of proteins overexpressed in Escherichia coli cells exclusively on the basis of information obtained in living cells. The protocol combines the preparation of the protein in E. coli cells, the rapid measurement of the three-dimensional (3D) NMR spectra by nonlinear sampling of the indirectly acquired dimensions, structure calculation and structure refinement. Under favorable circumstances, this in-cell NMR approach can provide high-resolution 3D structures of proteins in living environments. The protocol has been used to solve the first 3D structure of a protein in living cells for the putative heavy metal-binding protein TTHA1718 from Thermus thermophilus HB8 overexpressed in E. coli cells. As no protein purification is necessary, a sample for in-cell NMR measurements can be obtained within 2-3 d. With the nonlinear sampling scheme, the duration of each 3D experiment can be reduced to 2-3 h. Once chemical shift assignments and NOESY peak lists have been prepared, structure calculation with the program CYANA and energy refinement can be completed in less than 1 h on a powerful computer system.


Subject(s)
Escherichia coli/chemistry , Nuclear Magnetic Resonance, Biomolecular/methods , Proteins/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Carbon Isotopes , Computer Simulation , Escherichia coli/genetics , Models, Molecular , Nitrogen Isotopes , Protein Conformation , Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Software , Thermus thermophilus/chemistry , Thermus thermophilus/genetics
13.
J Virol ; 83(24): 12801-12, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19828620

ABSTRACT

White root rot, caused by the ascomycete Rosellinia necatrix, is a devastating disease worldwide, particularly in fruit trees in Japan. Here we report on the biological and molecular properties of a novel bipartite double-stranded RNA (dsRNA) virus encompassing dsRNA-1 (8,931 bp) and dsRNA-2 (7,180 bp), which was isolated from a field strain of R. necatrix, W779. Besides the strictly conserved 5' (24 nt) and 3' (8 nt) terminal sequences, both segments show high levels of sequence similarity in the long 5' untranslated region of approximately 1.6 kbp. dsRNA-1 and -2 each possess two open reading frames (ORFs) named ORF1 to -4. Although the protein encoded by 3'-proximal ORF2 on dsRNA-1 shows sequence identities of 22 to 32% with RNA-dependent RNA polymerases from members of the families Totiviridae and Chrysoviridae, the remaining three virus-encoded proteins lack sequence similarities with any reported mycovirus proteins. Phylogenetic analysis showed that the W779 virus belongs to a separate clade distinct from those of other known mycoviruses. Purified virions approximately 50 nm in diameter consisted of dsRNA-1 and -2 and a single major capsid protein of 135 kDa, which was shown by peptide mass fingerprinting to be encoded by dsRNA-1 ORF1. We developed a transfection protocol using purified virions to show that the virus was responsible for reduction of virulence and mycelial growth in several host strains. These combined results indicate that the W779 virus is a novel bipartite dsRNA virus with potential for biological control (virocontrol), named Rosellinia necatrix megabirnavirus 1 (RnMBV1), that possibly belongs to a new virus family.


Subject(s)
Ascomycota/virology , Pest Control, Biological , RNA Viruses/genetics , RNA, Double-Stranded/genetics , Amino Acid Motifs , Amino Acid Sequence , Ascomycota/growth & development , Ascomycota/pathogenicity , Base Sequence , Molecular Sequence Data , Open Reading Frames , RNA Viruses/chemistry , RNA Viruses/classification , RNA, Double-Stranded/chemistry , Transfection , Virion/genetics
14.
J Infect Chemother ; 15(2): 99-103, 2009 Apr.
Article in English | MEDLINE | ID: mdl-19396519

ABSTRACT

The purpose of this study was to clarify whether inhaled corticosteroids (ICSs) increased the infectious load of Chlamydophila pneumoniae and/or Mycoplasma pneumoniae in the respiratory tracts of asthmatic children. We studied a total of 310 outpatients with chronic stable asthma. Real-time polymerase chain reaction (PCR)-positive results for C. pneumoniae were obtained in 21 of 310 (6.8%) throat samples and 21 of 293 (7.2%) nasopharyngeal samples. There was no significant difference in the rate of detection or in the quantity of detection for C. pneumoniae between the ICS group and the non-ICS group, nor were there differences among groups classified by Japanese pediatric guidelines (JPGL) severity criteria. Real-time PCR-positive results for M. pneumoniae were obtained in 60 of 310 (19.4%) throat samples and 49 of 293 (16.7%) nasopharyngeal samples. There was no significant difference in the rate of detection or the quantity of detection between the ICS group and the non-ICS group, nor were there differences among age groups. The results of this research do not support the hypothesis that ICSs influence the infectious load of C. pneumoniae and M. pneumoniae. ICSs did not increase C. pneumoniae or M. pneumoniae infection in the upper respiratory tract, in contrast to the effect of ICSs in causing oral candidiasis. Our data exclude the concern that there is an increase in C. pneumoniae and M. pneumoniae infections due to ICS use, the use of ICSs being the gold standard in the long-term anti-inflammatory treatment of persistent asthma in children and adults.


Subject(s)
Adrenal Cortex Hormones/administration & dosage , Anti-Asthmatic Agents/administration & dosage , Asthma/drug therapy , Chlamydophila pneumoniae/drug effects , Mycoplasma pneumoniae/drug effects , Pharynx/microbiology , Administration, Inhalation , Adolescent , Adrenal Cortex Hormones/pharmacology , Adrenal Cortex Hormones/therapeutic use , Anti-Asthmatic Agents/pharmacology , Anti-Asthmatic Agents/therapeutic use , Chi-Square Distribution , Child , Child, Preschool , Chlamydophila pneumoniae/genetics , Chlamydophila pneumoniae/isolation & purification , Female , Humans , Infant , Male , Mycoplasma pneumoniae/genetics , Mycoplasma pneumoniae/isolation & purification , Nasopharynx/microbiology , Polymerase Chain Reaction
15.
Nature ; 458(7234): 102-5, 2009 Mar 05.
Article in English | MEDLINE | ID: mdl-19262674

ABSTRACT

Investigating proteins 'at work' in a living environment at atomic resolution is a major goal of molecular biology, which has not been achieved even though methods for the three-dimensional (3D) structure determination of purified proteins in single crystals or in solution are widely used. Recent developments in NMR hardware and methodology have enabled the measurement of high-resolution heteronuclear multi-dimensional NMR spectra of macromolecules in living cells (in-cell NMR). Various intracellular events such as conformational changes, dynamics and binding events have been investigated by this method. However, the low sensitivity and the short lifetime of the samples have so far prevented the acquisition of sufficient structural information to determine protein structures by in-cell NMR. Here we show the first, to our knowledge, 3D protein structure calculated exclusively on the basis of information obtained in living cells. The structure of the putative heavy-metal binding protein TTHA1718 from Thermus thermophilus HB8 overexpressed in Escherichia coli cells was solved by in-cell NMR. Rapid measurement of the 3D NMR spectra by nonlinear sampling of the indirectly acquired dimensions was used to overcome problems caused by the instability and low sensitivity of living E. coli samples. Almost all of the expected backbone NMR resonances and most of the side-chain NMR resonances were observed and assigned, enabling high quality (0.96 ångström backbone root mean squared deviation) structures to be calculated that are very similar to the in vitro structure of TTHA1718 determined independently. The in-cell NMR approach can thus provide accurate high-resolution structures of proteins in living environments.


Subject(s)
Bacterial Proteins/chemistry , Escherichia coli/cytology , Escherichia coli/metabolism , Nuclear Magnetic Resonance, Biomolecular/methods , Thermus thermophilus/genetics , Bacterial Proteins/genetics , Escherichia coli/genetics , Genes, Bacterial/genetics , Thermus thermophilus/chemistry
16.
Mycologia ; 101(1): 84-94, 2009.
Article in English | MEDLINE | ID: mdl-19271671

ABSTRACT

Rosellinia compacta is described as a new species that was discovered during a study of variation in Rosellinia necatrix in Japan using morphological and molecular characters. Rosellinia necatrix stromata and ascospores were 0.92-2.43 x 1.16-1.98 mm (mean 1.75 x 1.57 mm) and 30.5-55.9 x 5.0-10.3 microm (mean 41.8 x 6.9 microm) respectively. Rosellinia compacta had smaller stromata (1.13-1.71 x 0.99-1.36 mm; mean 1.43 x 1.16 mm) and longer ascospores ([34.0-]44.2-62.5 x 5.0-10.9 microm; mean 52.2 x 7.5 microm) than R. necatrix and also differs from other described species of Rosellinia.


Subject(s)
Ascomycota/classification , Plant Roots/microbiology , Analysis of Variance , Ascomycota/genetics , Ascomycota/isolation & purification , Ascomycota/pathogenicity , Cluster Analysis , DNA, Ribosomal Spacer/genetics , Hyphae/cytology , Japan , Phylogeny , Sequence Analysis , Species Specificity , Spores, Fungal/cytology
17.
Phytopathology ; 97(3): 278-86, 2007 Mar.
Article in English | MEDLINE | ID: mdl-18943646

ABSTRACT

ABSTRACT Rosellinia necatrix mycoreovirus 3 (W370) (RnMYRV-3/W370, described as RnMYRV-3 in this paper), a member of the newly established genus Mycoreovirus within the family Reoviridae, is the hypovirulence factor of the white root rot fungus, Rosellinia necatrix. Two virus-free fungal isolates (W37 and W97) that were somatically incompatible with the virus-harboring field isolate (W370) were transfected with purified RnMYRV-3 particles. Virus infection was confirmed by electrophoresis and northern hybridization of viral double-stranded RNA. RnMYRV-3 was transmissible from transfected strains to their respective, virus-free counterparts via hyphal anastomosis. Virus-transfected strains produced smaller lesions on apple fruits than did their virus-free counterparts. Virus-cured strains were indistinguishable from wild-type strains in culture morphology and displayed approximately the same virulence level on apples. Virus-transfected strains had "mosaic" colony portions consisting of thin, fast-growing and dense, slow-growing mycelia, and grew more slowly as a whole than their virus-free, parental strains. The level of virus accumulation varied among virus-transfected subcultures and within its single colonies. Virus-transfected strains were occasionally cured, as was W370. Such a phenomenon may be ascribed to uneven viral distribution in single colonies and the difficulty in viral transmission to virus-free hyphae.

18.
Masui ; 55(9): 1155-7, 2006 Sep.
Article in Japanese | MEDLINE | ID: mdl-16984014

ABSTRACT

BACKGROUND: When the applied cricoid pressure is too strong, or the place or direction of the pressure application is not appropriate, glottal closure may occur, but its details are unclear. METHODS: We evaluated possible changes in the size of the rima glottides due to backward pressure on the cricoid cartilage or backward pressure or backward, upward, and rightward pressure (BURP) on the thyroid cartilage using a video laryngoscope (Fine View' Laryngoscope, Tray Medical, Tokyo) in 6 adult males and 6 females with Cormack and Lehane grade 1. RESULTS: The right-to-left distance of the rima glottides was 5.1 +/- 1.2 mm without pressure application but was reduced to 3.8 +/- 1.7, 3.5 +/- 1.8, 2.8 +/- 1.9, 2.4 +/- 1.8, and 2.6 +/- 1.2 mm by 20 N and 30 N backward pressure on the cricoid cartilage and 20 N and 30 N backward pressure and BURP on the thyroid cartilage, respectively. Compared with the absence of pressure application, 20 N and 30 N backward pressure and BURP on the thyroid cartilage significantly reduced it. It was reduced to 1 mm by 30 N backward cricoid pressure in 1 patient while glottal closure occurred due to 30 backward thyroid pressure in 1 patient. CONCLUSIONS: The right-to-left distance of the rima glottides was significantly reduced by backward pressure or BURP on the thyroid cartilage, and was also markedly reduced by cricoid pressure in 1 of the 12 patients.


Subject(s)
Cricoid Cartilage/physiology , Glottis/pathology , Laryngoscopy , Laryngostenosis/etiology , Laryngostenosis/pathology , Pressure/adverse effects , Video Recording , Adult , Aged , Female , Humans , Intubation, Intratracheal/adverse effects , Male , Middle Aged , Pneumonia, Aspiration/etiology , Pneumonia, Aspiration/prevention & control
19.
Virus Res ; 118(1-2): 143-9, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16417937

ABSTRACT

We determined the complete nucleotide (nt) sequence (16,614 nt) of a large double-stranded (ds) RNA (referred to as L1 dsRNA), previously identified as the hypovirulence factor from strain V670 of the violet root rot fungus, Helicobasidium mompa. The positive-strand of L1 dsRNA contained a long open reading frame (ORF) potentially encoding a protein of 5,373 amino acids (molecular mass 603,080 Da) with conserved motifs characteristic of RNA-dependent RNA polymerase (RdRp) and helicase. The ORF is the longest so far reported in the fungal kingdom. The putative RdRp and helicase were shown to be related to putative RdRps and helicases of members of the genus Endornavirus. As is the case with endornaviruses, the coding (sense) strand of L1 dsRNA contained a discontinuity (nick) at nt position 2,552. A region between the RdRp and helicase domains of the polyprotein also had an amino acid sequence, resembling UDP glycosyltransferases (UGTs) in Oryza sativa endornavirus and Phytophthora endornavirus 1. Regions in the L1 dsRNA-encoded protein presumed to contain putative helicase, UGT and RdRp motifs were present at comparable positions to those in other endornaviruses. L1 dsRNA of H. mompa strain V670 was assigned to the genus Endornavirus, and here, we designate it as H. mompa endornavirus 1-670 (HmEV1-670). This represents the first report of a fungal endornavirus whose complete nucleotide sequence has been determined.


Subject(s)
Basidiomycota/virology , RNA Viruses/isolation & purification , RNA, Double-Stranded/genetics , Amino Acid Motifs/genetics , Amino Acid Sequence , Base Sequence , Gene Order , Genome, Viral , Glycosyltransferases/genetics , Molecular Sequence Data , Open Reading Frames , Phylogeny , RNA Helicases/genetics , RNA Viruses/genetics , RNA Viruses/pathogenicity , RNA, Double-Stranded/isolation & purification , RNA-Dependent RNA Polymerase/genetics , Sequence Alignment , Sequence Analysis, DNA , Sequence Homology , Synteny
20.
Masui ; 54(8): 875-80, 2005 Aug.
Article in Japanese | MEDLINE | ID: mdl-16104540

ABSTRACT

Continuous epidural administration of droperidol at 2.5 mg x day(-1) or less was performed in 837 patients after surgery. In 4 of these patients, an extrapyramidal reaction occurred. Patient 1 was a 10-year-old girl who developed the symptom 29 hours after the start of administration, with a total dose of 3.0 mg. Patient 2 was a 16-year-old girl in whom the symptom occurred 24 hours after the start, with a total of 5.3 mg. Patient 3 was a 22-year-old female with the symptom occurring 26 hours after the start, with a total of 5.2 mg. Patient 4 was a 74-year-old female in whom the symptom occurred 24 hours after the start, with a total of 1.3 mg. With respect to the age distribution, the total of 837 patients consisted of 16 patients aged 10 to 19 years, 85 patients aged 20 to 29 years, 91 patients aged 30 to 39 years, 90 patients aged 40 to 49 years, 77 patients aged 50 to 59 years, 148 patients aged 60 to 69 years, 240 patients aged 70 to 79 years, 97 patients aged 80 to 89 years, and 9 patients aged 90 to 99 years. Extrapyramidal reactions related to epidural administration may readily develop at younger ages.


Subject(s)
Antiemetics/adverse effects , Basal Ganglia Diseases/chemically induced , Droperidol/adverse effects , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Antiemetics/administration & dosage , Child , Dose-Response Relationship, Drug , Droperidol/administration & dosage , Female , Humans , Injections, Epidural , Postoperative Nausea and Vomiting/drug therapy
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