Home  About us  Contact
 

Repeat Analysis (repeat + analysis)

Distribution by Scientific Domains
Medical Sciences42%
Life Sciences42%

Kinds of Repeat Analysis

  • tandem repeat analysis
    		•

    Selected Abstracts

    Identification of the core element responsive to runt-related transcription factor 2 in the promoter of human type x collagen gene

    ARTHRITIS & RHEUMATISM, Issue 1 2009
    Akiro Higashikawa
    Objective Type X collagen and runt-related transcription factor 2 (RUNX-2) are known to be important for chondrocyte hypertrophy during skeletal growth and repair and development of osteoarthritis (OA) in mice. Aiming at clinical application, this study was undertaken to investigate transcriptional regulation of human type X collagen by RUNX-2 in human cells. Methods Localization of type X collagen and RUNX-2 was determined by immunohistochemistry, and their functional interaction was examined in cultured mouse chondrogenic ATDC-5 cells. Promoter activity of the human type X collagen gene (COL10A1) was examined in human HeLa, HuH7, and OUMS27 cells transfected with a luciferase gene containing a 4.5-kb promoter and fragments. Binding to RUNX-2 was examined by electrophoretic mobility shift assay and chromatin immunoprecipitation. Results RUNX-2 and type X collagen were co-localized in mouse limb cartilage and bone fracture callus. Gain and loss of function of RUNX-2 revealed that RUNX-2 is essential for type X collagen expression and terminal differentiation of chondrocytes. Human COL10A1 promoter activity was enhanced by RUNX-2 alone and more potently by RUNX-2 in combination with the coactivator core-binding factor , in all 3 human cell lines examined. Deletion, mutagenesis, and tandem repeat analyses identified the core responsive element as the region between ,89 and ,60 bp (termed the hypertrophy box [HY box]), which showed specific binding to RUNX-2. Other putative RUNX-2 binding motifs in the human COL10A1 promoter did not respond to RUNX-2 in human cells. Conclusion Our findings indicate that the HY box is the core element responsive to RUNX-2 in human COL10A1 promoter. Studies on molecular networks related to RUNX-2 and the HY box will lead to treatments of skeletal growth retardation, bone fracture, and OA. [source]

    Population divergence in the amphicarpic species Amphicarpaea edgeworthii Benth. (Fabaceae): microsatellite markers and leaf morphology

    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2009
    ZHONG-CHENG LIANG
    Comparative analyses of the genetic differentiation in microsatellite markers (FST) and leaf morphology characters (QST) of Amphicarpaea edgeworthii Benth. were conducted to gain insight into the roles of random processes and natural selection in the population divergence. Simple sequence repeat analyses on 498 individuals of 19 natural populations demonstrate that a significant genetic differentiation occurs among populations (mean FST = 0.578), and A. edgeworthii is a highly self-fertilized species (mean selfing rate s = 0.989). The distribution pattern of genetic diversity in this species shows that central populations possess high genetic diversity (e.g. population WL with HE = 0.673 and population JG with HE = 0.663), whereas peripheral ones have a low HE as in population JD (0.011). The morphological divergence of leaf shape was estimated by the elliptical Fourier analysis on the data from 11 natural and four common garden populations. Leaf morphology analyses indicate the morphological divergence does not show strong correlation with the genetic differentiation (R = 0.260, P = 0.069). By comparing the 95% confidence interval of QST with that of FST, QST values for five out of 12 quantitative traits are significantly higher than the average FST value over eight microsatellite loci. The comparison of FST and QST suggests that two kinds of traits can be driven by different evolutionary forces, and the population divergence in leaf morphology is shaped by local selections. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 505,516. [source]

    Frequent occurrence of multidrug-resistant CC17 Enterococcus faecium among clinical isolates in Sweden

    JOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2010
    H. Billström
    Abstract Aims:, To screen for the globally spread cluster of Enterococcus faecium, clonal complex 17 (CC17) and characterize the genetic profile of Swedish clinical Ent. faecium isolates. Methods:, A total of 203 consecutive isolates collected from 2004 to 2007 from patients with bacteraemia in Sweden. All isolates were genotyped using multiple-locus variable-number tandem repeat analysis (MLVA) and 20 isolates representing different MLVA types (MT) were chosen for multilocus sequence typing (MLST). Minimal inhibitory concentrations against clinically relevant antibiotics were determined with agar dilution. Presence of the virulence genes esp and hyl was investigated using PCR. Results:, A total of 65% (n = 109) of all isolates belonged to MT-1, and the second most common MLVA type was MT-159 (13%, n = 21). MLST analysis confirmed the presence of CC17 during the entire study period. The number of isolates resistant to gentamicin and vancomycin, as well as the presence of hyl, increased significantly during the investigation period. Conclusions:, The present study demonstrates that nosocomial infections caused by Ent. faecium CC17 are commonly occurring in Sweden. Significance and Impact of the Study:, This is the first report of CC17 Ent. faecium in Sweden. The increase of antibiotic resistance and virulence indicates that these strains are further adapting to the hospital environment. [source]

    A Forensic Laboratory Tests the Berkeley Microfabricated Capillary Array Electrophoresis Device,

    JOURNAL OF FORENSIC SCIENCES, Issue 4 2008
    Susan A. Greenspoon Ph.D.
    Abstract:, Miniaturization of capillary electrophoresis onto a microchip for forensic short tandem repeat analysis is the initial step in the process of producing a fully integrated and automated analysis system. A prototype of the Berkeley microfabricated capillary array electrophoresis device was installed at the Virginia Department of Forensic Science for testing. Instrument performance was verified by PowerPlex® 16 System profiling of single source, sensitivity series, mixture, and casework samples. Mock sexual assault samples were successfully analyzed using the PowerPlex® Y System. Resolution was assessed using the TH01, CSF1PO, TPOX, and Amelogenin loci and demonstrated to be comparable with commercial systems along with the instrument precision. Successful replacement of the Hjerten capillary coating method with a dynamic coating polymer was performed. The accurate and rapid typing of forensic samples demonstrates the successful technology transfer of this device into a practitioner laboratory and its potential for advancing high-throughput forensic typing. [source]

    Characterization of the 3p12.3-pcen region associated with tumor suppression in a novel ovarian cancer cell line model genetically modified by chromosome 3 fragment transfer

    MOLECULAR CARCINOGENESIS, Issue 12 2009
    Neal A.L. Cody
    Abstract The genetic analysis of nontumorigenic radiation hybrids generated by transfer of chromosome 3 fragments into the tumorigenic OV-90 ovarian cancer cell line identified the 3p12.3-pcen region as a candidate tumor suppressor gene (TSG) locus. In the present study, polymorphic microsatellite repeat analysis of the hybrids further defined the 3p12.3-pcen interval to a 16.1 Mb common region containing 12 known or hypothetical genes: 3ptel - ROBO2-ROBO1-GBE1-CADM2-VGLL3-CHMP2B-POU1F1-HTR1F-CGGBP1-ZNF654-C3orf38-EPHA3 -3pcen. Seven of these genes, ROBO1, GBE1, VGLL3, CHMP2B, CGGBP1, ZNF654, and C3orf38, exhibited gene expression in the hybrids, placing them as top TSG candidates for further analysis. The expression of all but one (VGLL3) of these genes was also detected in the parental OV-90 cell line. Mutations were not identified in a comparative sequence analysis of the predicted protein coding regions of these candidates in OV-90 and donor normal chromosome 3 contig. However, the nondeleterious sequence variants identified in the transcribed regions distinguished parent of origin alleles for ROBO1, VGLL3, CHMP2B, and CGGBP1 and cDNA sequencing of the hybrids revealed biallelic expression of these genes. Interestingly, underexpression of VGLL3 and ZNF654 were observed in malignant ovarian tumor samples as compared with primary cultures of normal ovarian surface epithelial cells or benign ovarian tumors, and this occurred regardless of allelic content of 3p12.3-pcen. The results taken together suggest that dysregulation of VGLL3 and/or ZNF654 expression may have affected pathways important in ovarian tumorigenesis which was offset by the transfer of chromosome 3 fragments in OV-90, a cell line hemizygous for 3p. Mol. Carcinog. © 2009 Wiley-Liss, Inc. [source]

    Genetic diversity in hazelnut (Corylus avellana L.) cultivars from Black Sea countries assessed using SSR markers

    PLANT BREEDING, Issue 4 2010
    K. Gürcan
    With 6 figures and 6 tables Abstract European hazelnut (Corylus avellana L.) is an important crop in Turkey, Georgia and Azerbaijan, where cultivars were selected from the native vegetation. Accessions from Turkey have been assigned to the Black Sea group, and cultivars from Georgia and Azerbaijan have a similar phenotype. Genetic diversity was investigated in 88 accessions from these three countries and compared with cultivars from Spain and Italy using 12 microsatellite loci. A high level of genetic diversity (He = 0.71, Ho = 0.70) was observed in the Black Sea accessions. Six Turkish accessions in the US hazelnut collections were found to be synonyms of cultivars in the Turkish collection in Giresun. An unweighted pair-group method using arithmetic average dendrogram and principal component analysis of 109 unique accessions showed a tendency to form subgroups by country of origin, and high diversity within each subgroup. A moderate shift in allelic frequencies (FST = 0.114,0.131) was seen between accessions from the Black Sea and the Spanish-Italian accessions. Simple sequence repeat analysis identified the putative parents of two Turkish cultivars. [source]

    Molecular epidemiology of the nasal colonization by methicillin-susceptible Staphylococcus aureus in Swiss children

    CLINICAL MICROBIOLOGY AND INFECTION, Issue 9 2010
    C. Mégevand
    Clin Microbiol Infect 2010; 16: 1414,1420 Abstract Nasal carriage of Staphylococcus aureus contributes to an increased risk of developing an infection with the same bacterial strain. Genetic regulatory elements and toxin-expressing genes are virulence factors associated with the pathogenic potential of S. aureus. We undertook an extensive molecular characterization of methicillin-susceptible S. aureus (MSSA) carried by children. MSSA were recovered from the nostrils of children. The presence of Panton-Valentine leukocidin (PVL), exfoliatins A and B (exfoA and exfoB), and the toxic-shock staphylococcal toxin (TSST-1) and agr group typing were determined by quantitative PCR. A multiple-locus variable-number of tandem repeat analysis (MLVA) assay was also performed for genotyping. Five hundred and seventy-two strains of MSSA were analysed. Overall, 30% were positive for toxin-expressing genes: 29% contained one toxin and 1.6% two toxins. The most commonly detected toxin gene was tst, which was present in 145 (25%) strains. The TSST-1 gene was significantly associated with the agr group 3 (OR 56.8, 95% CI 32.0,100.8). MLVA analysis revealed a large diversity of genetic content and no clonal relationship was demonstrated among the analysed MSSA strains. Multilocus sequence typing confirmed this observation of diversity and identified ST45 as a frequent colonizer. This broad diversity in MSSA carriage strains suggests a limited selection pressure in our geographical area. [source]