OBJECTIVETo type and group the Yersinia pestis strains isolated in China to clarify the geographical distribution of ribotypes of Yersinia pestis.

METHODSGenomic DNA of Yersinia pestis were digested with EcoR I, then hybridized with 16s-23s-5s rRNA gene probe.

RESULTSThese tested strains were divided into 3 ribotypes, the profiles obtained were relatively homogeneous, with most of them differed only by the presence or the absence of 1 - 2 restriction fragments. Ribotype A and B were the most common types, which distributed in a large area in China while ribotype C was the least, only limited to a small area. There was certain correlation between the ribotypes and the plague foci, usually only one ribotype was found in one plague foci.

CONCLUSIONThe ribotypes were stable in the plague foci. Correlation between the ribotypes of Yersinia pestis strains and their geographical origins was noticed. All 3 ribotypes had different origins, however ribotype A and ribotype C seemed to be closer related.

China ; DNA, Bacterial ; genetics ; Geography ; RNA, Ribosomal, 16S ; genetics ; RNA, Ribosomal, 23S ; genetics ; RNA, Ribosomal, 5S ; genetics ; Ribotyping ; Yersinia pestis ; classification ; genetics

Objective To describe the microbiological characteristics of ()CGMCC 12426 and determine and analyze its complete genome sequences.Methods strain CGMCC 12426 genomic DNA sequencing was performed on a single molecule real-time sequencing(SMRT)platform and the annotation was completed in the NCBI Prokaryotic Genomic Annotation Pipeline(pGAP).Results The complete genomic sequences of the released CGMCC 12426 consisted of a 4 138 265-bp circular chromosome and a 74 165-bp plasmid,which resulted in the prediction of 4581 genes including 4222 coding sequences,87 tRNAs,and 30 rRNAs(which included 5S rRNA,16S rRNA,and 23S rRNA).Conclusion The genome sequencing provided a basis for further investigations on the genetic background of and on the metabolic and regulatory mechanisms.
Bacillus subtilis ; genetics ; Genome, Bacterial ; Plasmids ; RNA, Ribosomal, 16S ; genetics ; RNA, Ribosomal, 23S ; genetics ; RNA, Ribosomal, 5S ; genetics ; Sequence Analysis, DNA

OBJECTIVETo investigated the genetic polymorphism of the isolated strains using ribotyping method.

METHODSOne hundred twenty-two strains of V. cholerae O139 isolated from different areas of China from 1993 to 1999 were selected and characterized with ribotyping, including 16s rDNA and 23s rDNA probes.

RESULTSOne hundred twenty-two strains were differentiated into 10 different ribotypes (RT1-RT10) on the basis of rRNA gene probes hybridization (with Bgl I digestion), which consisted of 7 - 9 bands between 12 and 1.5 kb in size. RT1 and RT3, as two predominant ribotypes, comprised most number of the strains which spread to the extensive range. Nine strains, which are negative to ctxAB, zot and RS individually, belong to 4 special ribotypes. The dendrogram revealing genetic relationship among different clones of V. cholerae O139 showed that the clones belonging to RT1 and RT2 had genetic similarity on high degree, although they were isolated from different regions. The two predominant ribotypes (RT1 and RT3) were distant in genetic relationship.

CONCLUSIONResults showed the clonal diversity and the wide area distribution of V. cholerae O139 strains in China, suggesting the multiple origins of O139 epidemics.

Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S ; genetics ; RNA, Ribosomal, 23S ; genetics ; Ribotyping ; Species Specificity ; Vibrio cholerae O139 ; classification ; genetics

The total sequence of 18S rRNA and the neighbours including 1950 pairs of nucleotide (N) was received by PCR and expressed orderly. The examinated sample was 1 of 8 adult worms collected from 12.5 years old male patient. The worm was determined morphologically as Fasciolopsis buski. The comparison showed that in this intestinal fluke worm there is an almost absolutely analogous coefficient concerning nitrogen components of 18S rRNA in only 2 differences on 1950 N (0.01%) with the gene sequence of 18S rRNA kept in the bank of genes. In Viet Nam, this is the first molecular determination realized on human
Fasciolidae ; Trematoda ; RNA, Ribosomal, 18S

The paper is aimed to identify SNP in Sarcandra glabra and Chloranthus spicatus, and authenticate S. glabra from Ch. spicatus and the mixture by using PCR amplification of specific alleles. SNPs in the ITS sequences of S. glabra and Ch. spicatus were found by ClustulX 2. 1 program and Bioedit software. Primers for authentic S. glabra and Ch. spicatus was designed according to the SNP site, and ITS sequence universal primers plus to the authentic primer to construct a multi-PCR reaction system, and then optimized the PCR reaction system. Five hundred and eighty band special for S. glabra and 470 bp band special for Ch. spicatus were found by using multi-PCR reaction. The multi-PCR reaction system could be applied to identify S. glabra and Ch. spicatus's leaves.
DNA, Plant ; analysis ; genetics ; DNA, Ribosomal ; genetics ; DNA, Ribosomal Spacer ; analysis ; genetics ; Magnoliopsida ; classification ; genetics ; Plant Leaves ; genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; RNA, Ribosomal ; genetics ; RNA, Ribosomal, 18S ; genetics ; RNA, Ribosomal, 5.8S ; genetics ; Species Specificity

Soil archaea and fungi play important roles in the greenhouse soil ecosystem. To develop and apply rich microbial resources in greenhouse ecological environment, and to understand the interaction between microbes and plants, we constructed archaeal 16S rRNA and fungal 18S rRNA gene libraries to analyze the compositions of archaeal and fungal communities. Total greenhouse soil DNA was directly extracted and purified by skiving-thawing-lysozyme-proteinase K-SDS hot treatment and treatment of cetyltriethylammnonium bromide (CTAB). After PCR amplification, retrieving, ligating, transforming, screening of white clones, archaeal 16S rRNA and fungal 18S rRNA gene libraries were constructed. The sequences of archaea and fungi were defined into operational taxonomic units (OTUs) when 97% similarity threshold for OTU assignment was performed by using the software DOTUR. Phylogenetic analysis showed that crenarchaeota and unidentified-archaea were the two major sub-groups and only a few of euryarchaeota existed in the archaeal clone library, total 45 OTUs. All the crenarchaeota belonged to thermoprotei; except for Basidiomycotina, the other four sub-group fungi were discovered in the fungal library, total 24 OTUs. The diversities of archaea were very abundant and a few euryarchaeota (methanebacteria) existed in the archaeal clone library, it might be directly related to the long-term high temperature, high humidity, and high content of organic matter. The limitation of oxygen was the other reason for causing this phenomenon; Ascomycotina (over 80%) was the dominant sub-groups in fungal library. It was because most of the plant fungal diseases belonged to soil-borne diseases which gone through the winter by the ways of scierotium or perithecium and became the sources of primary infection.
Archaea ; genetics ; growth & development ; Biodiversity ; Cloning, Molecular ; Cucumis sativus ; growth & development ; Fungi ; genetics ; growth & development ; Gene Library ; Genes, rRNA ; Microclimate ; Phylogeny ; Plant Roots ; microbiology ; RNA, Archaeal ; genetics ; RNA, Fungal ; genetics ; RNA, Ribosomal, 16S ; genetics ; RNA, Ribosomal, 18S ; genetics ; Soil Microbiology

Ribosomal RNAs are important because they catalyze the synthesis of peptides and proteins. Comparative studies of the secondary structure of 18S rRNA have revealed the basic locations of its many length-conserved and length-variable regions. In recent years, many more sequences of 18S rDNA with unusual lengths have been documented in GenBank. These data make it possible to recognize the diversity of the secondary and tertiary structures of 18S rRNAs and to identify the length-conserved parts of 18S rDNAs. The longest 18S rDNA sequences of almost every known eukaryotic phylum were included in this study. We illustrated the bioinformatics-based structure to show that, the regions that are more length-variable, regions that are less length-variable, the splicing sites for introns, and the sites of A-minor interactions are mostly distributed in different parts of the 18S rRNA. Additionally, this study revealed that some length-variable regions or insertion positions could be quite close to the functional part of the 18S rRNA of Foraminifera organisms. The tertiary structure as well as the secondary structure of 18S rRNA can be more diverse than what was previously supposed. Besides revealing how this interesting gene evolves, it can help to remove ambiguity from the alignment of eukaryotic 18S rDNAs and to improve the performance of 18S rDNA in phylogenetic reconstruction. Six nucleotides shared by Archaea and Eukaryota but rarely by Bacteria are also reported here for the first time, which might further support the supposed origin of eukaryote from archaeans.
Animals ; Base Sequence ; Drosophila melanogaster ; genetics ; Eukaryota ; classification ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 16S ; chemistry ; genetics ; RNA, Ribosomal, 18S ; chemistry ; classification ; genetics ; Sequence Alignment ; Sequence Analysis, RNA ; Thermus thermophilus ; genetics

OBJECTIVETo establish the approach to detecting two biovars of Ureaplasma urealyticum (Uu) in human semen and to investigate the relationship between the two biovars of Uu infection and the quality of human semen.

METHODSBased on the 16S-23S rRNA intergenic spacer region, three pairs of primers were designed, the species specific primer and two biovars primers (Parvo primer and T960 primer). The two biovars of Uu were detected in the semen from 949 men by semen culture and PCR assay. Meanwhile, semen routine analyses were performed.

RESULTSIn the 949 subjects, 199 were Uu positive both in Uu liquid culture and PCR assay (199/949, 21.1%), of which 136 (136/199, 68.3%) were Parvo biovar, 54 (54/199, 27.1%) T960 biovar, and 9 (9/199, 4.5%) both Parvo and T960 biovars. Compared with the Parvo and the negative groups, human sperm viability was significantly decreased (P < 0.05 ) in the Uu T960 infection group. The difference of sperm motility and density had no statistic significance.

CONCLUSIONA significant correlation has been found between Uu T960 biovar infection and human sperm viability

Adult ; Humans ; Male ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; genetics ; RNA, Ribosomal, 23S ; genetics ; Semen ; microbiology ; Sperm Motility ; Ureaplasma urealyticum ; classification ; genetics

We attempted to identify parasite DNA in the biliary stones of humans via PCR and DNA sequencing. Genomic DNA was isolated from each of 15 common bile duct (CBD) stones and 5 gallbladder (GB) stones. The patients who had the CBD stones suffered from cholangitis, and the patients with GB stones showed acute cholecystitis, respectively. The 28S and 18S rDNA genes were amplified successfully from 3 and/or 1 common bile duct stone samples, and then cloned and sequenced. The 28S and 18S rDNA sequences were highly conserved among isolates. Identity of the obtained 28S D1 rDNA with that of Clonorchis sinensis was higher than 97.6%, and identity of the 18S rDNA with that of other Ascarididae was 97.9%. Almost no intra-specific variations were detected in the 28S and 18S rDNA with the exception of a few nucleotide variations, i.e., substitution and deletion. These findings suggest that C. sinensis and Ascaris lumbricoides may be related with the biliary stone formation and development.
Aged ; Aged, 80 and over ; Animals ; Ascaridida/genetics/isolation & purification ; Ascaris lumbricoides/genetics/isolation & purification ; Base Sequence ; Clonorchis sinensis/genetics/isolation & purification ; Common Bile Duct/*parasitology ; DNA, Helminth/*genetics ; DNA, Ribosomal/genetics ; Face/parasitology ; Female ; Gallbladder/parasitology ; Gallstones/*parasitology ; Helminths/genetics/*isolation & purification ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment

Because of an increased number of Acanthamoeba keratitis (AK) along with associated disease burdens, medical professionals have become more aware of this pathogen in recent years. In this study, by analyzing both the nuclear 18S small subunit ribosomal RNA (18S rRNA) and mitochondrial 16S rRNA gene loci, 27 clinical Acanthamoeba strains that caused AK in Japan were classified into 3 genotypes, T3 (3 strains), T4 (23 strains), and T5 (one strain). Most haplotypes were identical to the reference haplotypes reported from all over the world, and thus no specificity of the haplotype distribution in Japan was found. The T4 sub-genotype analysis using the 16S rRNA gene locus also revealed a clear sub-conformation within the T4 cluster, and lead to the recognition of a new sub-genotype T4i, in addition to the previously reported sub-genotypes T4a-T4h. Furthermore, 9 out of 23 strains in the T4 genotype were identified to a specific haplotype (AF479533), which seems to be a causal haplotype of AK. While heterozygous nuclear haplotypes were observed from 2 strains, the mitochondrial haplotypes were homozygous as T4 genotype in the both strains, and suggested a possibility of nuclear hybridization (mating reproduction) between different strains in Acanthamoeba. The nuclear 18S rRNA gene and mitochondrial 16S rRNA gene loci of Acanthamoeba spp. possess different unique characteristics usable for the genotyping analyses, and those specific features could contribute to the establishment of molecular taxonomy for the species complex of Acanthamoeba.
Acanthamoeba/classification/genetics/growth & development/*isolation & purification ; Acanthamoeba Keratitis/*parasitology ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/genetics ; Humans ; Japan ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics