MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.
Classification* ; Interspersed Repetitive Sequences ; MicroRNAs* ; RNA, Messenger

Bacterial Typing Techniques ; China ; Humans ; Interspersed Repetitive Sequences ; Mycobacterium tuberculosis ; classification ; genetics ; isolation & purification ; Ribotyping

OBJECTIVES: Integrons are thought to play an important role in the spread of antibiotic resistance. This study investigates class 1 and 2 integron-positive methicillin-resistant coagulase-negative staphylococci strains isolated in Iran and characterizes their patterns of antimicrobial resistance. METHODS: Hundred clinical isolates of coagulase-negative staphylococci were characterized for integron content and staphylococcal cassette chromosome mec (SCCmec) type. RESULTS: Sixteen isolates carried class 1 (intI1) integrons and four isolates carried class 2 (intI2) integrons. One resistance gene array was identified among the class 1 integrons (aadA1 cassette). The distribution of SCCmec types in 50 methicillin-resistant coagulase-negative staphylococci strains showed that SCCmec types III and V dominated among the tested strains. CONCLUSION: This is the first report of methicillin-resistant coagulase-negative staphylococci strains that carry two mobile genetic elements, including class 1 and 2 integrons and SCCmec, in Iran.
Coagulase* ; Drug Resistance, Microbial ; Integrons* ; Interspersed Repetitive Sequences ; Iran ; Methicillin Resistance*

BACKGROUND: Single-nucleotide polymorphism (SNP) analysis is a powerful strategy for large-scale molecular population studies examining phylogenetic relationships among bacterial strains. Mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) can be easily digitized to share data among laboratories. This study applied SNP and MIRU-VNTR analyses for molecular strain typing of Mycobacterium tuberculosis isolates collected throughout Korea. METHODS: We studied 102 clinical M. tuberculosis isolates, including 6 paired strains, collected from 11 university hospitals in Korea in 2008 and 2009. SNPs were detected using hairpin primer assays, and then, MIRU-VNTR analysis was performed. RESULTS: Thirty-five SNPs contained polymorphisms that helped differentiate the 96 tested isolates. The isolates were classified into 15 clusters. The Beijing family strains were distributed within closely related clusters in the SNP dendrogram. For MIRU-VNTR analysis, the 96 isolates were divided into 12 groups. The discriminatory index in 8 of these groups (MIRU-10, -23, -26, and -31; ETR-A, -B, -C, and -F) was high (Hunter-Gaston diversity index > 0.6). Unlike the SNP method, MIRU-VNTR analysis did not identify any notable localizations of Beijing or non-Beijing family isolates in specific clusters. CONCLUSIONS: SNP and MIRU-VNTR analyses are surrogate molecular strain-typing methods for M. tuberculosis in Korea where Beijing family isolates are predominant.
Cluster Analysis ; DNA Primers/chemistry ; Interspersed Repetitive Sequences ; *Minisatellite Repeats ; Mycobacterium tuberculosis/*classification/genetics/isolation & purification ; Phylogeny ; *Polymorphism, Single Nucleotide ; Republic of Korea

BACKGROUND: Mycobacterial Interspersed Repetitive Units (MIRUs) that are located mainly in intergenic regions dispersed throughout the Mycobacterium tuberculosis genome. The selected MIRU loci, which were composed of a 12-locus set, demonstrated a high power for discrimination of Mycobacterium tuberculosis isolates collected from Kangwon province of Korea. To evaluate its ability to discriminate the M. tuberculosis strains, 45 clinical isolates were genotyped using the methods IS6110 RFLP and MIRU. METHODS: All the samples were collected during the period from January 2007 to December 2007 from TB patients, who were residents and registered to a public health center of Kangwon Province in Korea. A total of 45 DNAs were extracted from clinical isolated mycobacterial strains and genotyped using IS6110 RFLP, the MIRU method. RESULTS: We compared the 12-MIRU with IS6110 RFLP in the 45 samples, the 12-locus version offered less discriminatory power (Hunter-Gaston discriminatory index [HGDI]: 0.959 vs 0.998; 57.78% of clustered cases vs 8.89%). CONCLUSION: This 12-locus MIRU can be useful when additional combinations of other loci for genotyping M. tuberculosis in Korea where the Beijing family strains are dominant.
Discrimination (Psychology) ; DNA ; DNA, Intergenic ; Genome ; Genotype ; Humans ; Interspersed Repetitive Sequences ; Korea ; Mycobacterium ; Mycobacterium tuberculosis ; Polymorphism, Restriction Fragment Length ; Public Health ; Tuberculosis

We selected and characterized isolates of Lactobacillus crispatus (L. crispatus) for potential preventing infections of the female reproductive tract. We cultured vaginal swabs from healthy volunteers on de Man, Rogosa and Sharpe (MRS) agar and identified the isolates at the species level by 16S rRNA sequence and genotyped the isolates of Lactobacillus by PCR amplification of repetitive bacterial DNA elements (rep-PCR). Furthermore, 10 L. crispatus strains were assessed for hydrogen peroxide (H2O2) and acid production. Overall 65 isolates were confirmed to be Lactobacillus by sequence analogy, among them 19 were L. crispatus, 17 were Lactobacillus jensenii and 12 were Lactobacillus fermentum. rep-PCR produced specie and strain-specific genomic fingerprints for the Lactobacillus isolates. The selected 10 L. crispatus isolates produced highly acidic environment after growth in MRS. The isolates T22-3 and T29-5 demonstrated high production of H2O2. This study indicated that there are individual differences with vaginal Lactobacillus colonization, and strain diversity within vaginal L. crispatus isolates, T22-3 and T29-5 might be candidates for restoring urogenital health environment in females.
Adult ; Female ; Genotype ; Humans ; Hydrogen Peroxide ; metabolism ; Interspersed Repetitive Sequences ; Lactobacillus ; classification ; genetics ; isolation & purification ; physiology ; Polymerase Chain Reaction ; methods ; Vagina ; microbiology

"Wu zhu yu", which is obtained from the dried unripe fruits of Tetradium ruticarpum (A. Jussieu) T. G. Hartley, has been used as a traditional Chinese medicine for treatment of headaches, abdominal colic, and hypertension for thousands of years. The present study was designed to assess the molecular genetic diversity among 25 collected accessions of T. ruticarpum (Wu zhu yu in Chinese) from different areas of China, based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Thirteen ISSR primers generated 151 amplification bands, of which 130 were polymorphic. Out of 165 bands that were amplified using 10 iPBS primers, 152 were polymorphic. The iPBS markers displayed a higher proportion of polymorphic loci (PPL = 92.5%) than the ISSR markers (PPL = 84.9%). The results showed that T. ruticarpum possessed high loci polymorphism and genetic differentiation occurred in this plant. The combined data of iPBS and ISSR markers scored on 25 accessions produced five clusters that approximately matched the geographic distribution of the species. The results indicated that both iPBS and ISSR markers were reliable and effective tools for analyzing the genetic diversity in T. ruticarpum.
Base Sequence ; Binding Sites ; DNA Fingerprinting ; DNA Primers ; metabolism ; DNA, Plant ; genetics ; isolation & purification ; Evodia ; classification ; genetics ; Genetic Markers ; genetics ; Genetic Variation ; Interspersed Repetitive Sequences ; genetics ; Phylogeny ; Polymorphism, Genetic ; Random Amplified Polymorphic DNA Technique ; Terminal Repeat Sequences ; genetics

OBJECTIVETo finish the work of sequencing the full sequence of intron 51 of dystrophin gene and understand its characteristic of sequence.

METHODSThe whole intron 51 was sequenced by primer walking. The sequencing results were analyzed by repeat sequences, matrix attachment region (MAR) and topoisomerase II cleavage sites. The residue sequences, after removal of the repetitive sequences, were subjected to the analysis of CpG islands, promoter, open reading frame (ORF) and unidentified low copy repeat sequence.

RESULTSThe acquired intron 51 sequence was composed of 38725 bp. Repetitive sequences constituted 37.53% of total intron sequence. The overall G+C content of intron 51 was 36.34%. There are four potential MARs in intron 51. Three of them are clustered in the 12 kb region near exon 51. Numerous ORFs were found on both strands, but no homologues proteins were found in Genbank CDS transcriptional peptide, PDB, SwissProt, PIR and PRF databases.

CONCLUSIONThe expansion of intron 7 over the last 120 million years was mainly the result of L1 insertion into intron 7, and not all of repetitive sequences are associated with chromosomal rearrangement. No sequence of functional significance was found in intron 51. The results suggest that the cluster of MARs may be associated with the instability of intron 51.

Base Sequence ; CpG Islands ; genetics ; Databases, Nucleic Acid ; Dystrophin ; genetics ; Gene Deletion ; Genes ; Humans ; Introns ; genetics ; Long Interspersed Nucleotide Elements ; genetics ; Mutagenesis, Insertional ; Open Reading Frames ; Promoter Regions, Genetic ; Repetitive Sequences, Nucleic Acid ; genetics ; Sequence Analysis, DNA ; methods

OBJECTIVETo explore the molecular-epidemiology of Mycobacterium tuberculosis in Shanghai.

METHODSDrug-resistant and drug-susceptible strains of M. tuberculosis were randomly selected from the bank of M. tuberculosis of Shanghai Municipal Center for Disease Control and Prevention and were genotyped by mycobacterial interspersed repetitive units(MIRU) and Spoligotyping methods. The genotyping results were analyzed and combined with epidemiological data.

RESULTSThe Spoligotyping results demonstrated that 89 % (81/91) of the strains belonged to the Beijing genotype. Of the patients who had received BCG-vaccination,88.5% (54/61) infected with strains of Beijing genotype and 90.0% (27/30) of the patients were not BCG-vaccinated. However, the difference was not statistically significant. Drug-resistant rate from those strains of Beijing genotype was 45.7 (37/81), lower than that of non-Beijing genotype (60.0% ,6/10). Again,the difference was not statistically significant. The MIRU results showed that 62.6 % (57/91) were strains of clusters.

CONCLUSIONThe Beijing genotype of M. tuberculosis were found to be the dominant strains in Shanghai. The associations between Beijing genotype strains and BCG vaccination or drug-resistant were not found. Results from cluster analysis suggested that some cases might belong to the newly developed cases.

Adolescent ; Adult ; Aged ; Aged, 80 and over ; China ; Drug Resistance, Bacterial ; Female ; Genotype ; Humans ; Interspersed Repetitive Sequences ; Male ; Middle Aged ; Mycobacterium bovis ; immunology ; Mycobacterium tuberculosis ; genetics ; isolation & purification ; Tuberculosis ; epidemiology ; prevention & control ; Vaccination ; Young Adult

Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as 180degrees and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed.
DNA End-Joining Repair ; DNA Transposable Elements ; DNA* ; Enhancer Elements, Genetic ; Hand ; Homologous Recombination ; Retroelements