Trypanosomatidae:PhytomonasDetection in Plants and Phytophagous Insects by PCR Amplification of a Genus-Specific Sequence of the Spliced Leader Gene

1999 ◽  
Vol 91 (3) ◽  
pp. 268-279 ◽  
Author(s):  
Myrna G. Serrano ◽  
Luiz R. Nunes ◽  
Marta Campaner ◽  
Gregory A. Buck ◽  
Erney P. Camargo ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Phytophagous Insects ◽  
Specific Sequence ◽  
Spliced Leader

scholarly journals PCR amplification of the spliced leader gene for the diagnosis of trypanosomatid parasites of plants and insects in methanol-fixed smears

1999 ◽  
Vol 176 (1) ◽  
pp. 241-246 ◽  
Author(s):  
Myrna G. Serrano ◽  
Marta Campaner ◽  
Gregory A. Buck ◽  
Marta M.G. Teixeira ◽  
Erney Plessmann Camargo
Keyword(s):  
Pcr Amplification ◽  
Spliced Leader ◽  
Trypanosomatid Parasites

RAPD analysis of jasmine rice-specific genomic structure

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 716-719 ◽  
Author(s):  
Y J Wu ◽  
Y Chen ◽  
J Wang ◽  
C X Zhu ◽  
B L Xu
Keyword(s):  
Oryza Sativa L ◽  
Genomic Structure ◽  
Pcr Amplification ◽  
Disease Resistance Gene ◽  
Japonica Rice ◽  
Rice Seed ◽  
Specific Sequence ◽  
First Intron ◽  
Jasmine Rice ◽  
True Relation

Total genomic DNA was extracted from 29 samples of rice seed, including jasmine rice Oryza sativa L. subsp indica 'KDML105', 'KDML105'-derived varieties, nonaromatic Thailand rice, and japonica rice. Polymorphism in RAPD profiles was analyzed to explore the genomic structure specific to jasmine rice. The degree of band sharing was used to evaluate genetic distance between varieties and to construct a phylogenetic tree. RD15, CNTLR85033, and CNT87040 were found to be closest to 'KDML105', which was consistent with the true relation among them. Four RAPD fragments that cooperatively distinguished jasmine rice from others were cloned and sequenced. PCR amplification using pairs of primers designed specifically further confirmed the credibility of the RAPD result. Comparison through Genbank revealed that a 454 bp RAPD band was similar to the first intron of a putative Cf2/Cf5 disease resistance gene and a 1107 bp RAPD band similar to a wall-associated kinase (wak) gene sequence.Key words: Jasmine rice, RAPD, specific sequence.

scholarly journals Phenotypic and molecular characterization of HA-MRSA in Taif hospitals, Saudi Arabia

2015 ◽  
Vol 9 (03) ◽  
pp. 298-303 ◽  
Author(s):  
Emad M Eed ◽  
Mabrouk M Ghonaim ◽  
Yousry M Hussein ◽  
Taiser M Saber ◽  
Amany S Khalifa
Keyword(s):  
Saudi Arabia ◽  
Gene Polymorphism ◽  
Pcr Amplification ◽  
Clinical Samples ◽  
Molecular Characteristics ◽  
Polymorphism Analysis ◽  
Specific Sequence ◽  
Mrsa Strains ◽  
Hospital Acquired ◽  
Sccmec Types

Introduction: Methicillin-resistant S. aureus (MRSA) is one of the most important organisms causing hospital-acquired infections worldwide. Molecular analysis of MRSA strains from Taif, Saudi Arabia, had not been previously done. Phenotypic and molecular characteristics of MRSA isolated from Taif hospitals were investigated. Methodology: This study involved S. aureus strains isolated from different clinical samples from Taif hospitals. MRSA strains were identified and antimicrobial susceptibility profiles were determined. Multiplex polymerase chain reaction (PCR) was used to identify S. aureus-specific sequence, mecA genes, and type of staphylococcal cassette chromosome mec (SCCmec). MRSA strains were typed using coagulase gene polymorphism. Results: In total, 390 strains of S. aureus were isolated, and 58 MRSA strains – 40 hospital-acquired  MRSA (HA-MRSA) and 18 community-acquired MRSA (CA-MRSA) – were detected. HA-MRSA strains included three SCCmec types, while CA-MRSA strains included two SCCmec types. PCR amplification and restriction of the coagulase gene of the 58 MRSA isolates showed nine different patterns, while three strains were non-typable. HA-MRSA strains showed seven distinct restriction fragment length polymorphism (RFLP) patterns; the most frequent was pattern 2 (15 isolates), followed by patterns 1 and 4 (5 isolates each). CA-MRSA showed five RFLP patterns; the most frequent was pattern 3 (7 isolates) followed by pattern 8 (6 isolates). Conclusions: HA-MRSA strains were more common than CA-MRSA strains. SCCmec typing and coagulase gene polymorphism analysis may be useful methods for studying clonal relatedness of isolates and for discriminating between HA-MRSA and CA-MRSA.

Sex identification from exfoliated primary teeth - a PCR study

2006 ◽  
Vol 30 (1) ◽  
pp. 19-21 ◽  
Author(s):  
Manju Gopa Kumar ◽  
Amitha Hegde
Keyword(s):  
Primary Teeth ◽  
Pcr Amplification ◽  
Extraction Methods ◽  
The Body ◽  
Proteinase K ◽  
Deciduous Teeth ◽  
Pulp Tissue ◽  
Specific Sequence ◽  
Dental Pulp Tissue ◽  
Template Dna

Teeth endure postmortem degradation and extreme changes in ambient temperature and pressure better than most human tissues. In the present day scenario the growing number of crime against children in the form of battering, physical/sexual abuse, abduction and kidnapping, the use of exfoliated primary teeth, become many times the only evidence available at the crime scene. Despite exposure of the body to burial, mutilation, explosion or incineration, it is usually possible to extract DNA from pulp tissue of tooth with sufficient quality and quantity. Hence the present study was undertaken to find out the sex of a child from exfoliated/extracted deciduous teeth using a Polymerase Chain reaction(PCR) based analysis. Tooth samples were stored in room temperature after double coding for various periods. Dental pulp tissue was collected from each sample and DNA was isolated by proteinase-k digestion and phenol chloroform extraction methods. PCR amplification was done with two sets of oligonucleiotide primers. Amplification of X (131bp) and Y-specific sequences (172bp) in males and that of the X-specific sequence in females was observed and compared with the template DNA showing male and female controls. Determination of sexes of all freshly collected samples within 24 hours and after 1 month of extraction respectively gave 100% result. However, PCR was not found to be an effective method for sex determination after 6 months post extraction.

scholarly journals Direct Detection of eae-Positive Bacteria in Human and Veterinary Colorectal Specimens by PCR

1998 ◽  
Vol 36 (8) ◽  
pp. 2326-2330 ◽  
Author(s):  
A. L. Hubbard ◽  
D. J. Harrison ◽  
C. Moyes ◽  
S. McOrist
Keyword(s):  
Direct Detection ◽  
Pcr Amplification ◽  
Enteric Bacteria ◽  
Quick Method ◽  
Specific Sequence ◽  
Reading Frame ◽  
E Coli ◽  
Associated Lesions ◽  
Reference Strains ◽  
Pcr Test

A PCR test based on the amplification of aneae-specific sequence was designed and evaluated for its ability to directly detect homologous sequences in enteropathogenicEscherichia coli and Citrobacter spp. (amplification of eae open reading frame, 178 bp) in sections of the intestines of humans and animals with colonic lesions. Positive PCR results were observed with eae-positive reference strains of E. coli and Citrobacter rodentium (Citrobacter freundii biotype 4280). Known eae-negative reference strains of E. coli and other laboratory strains of enteric bacteria were negative by the amplification test. The sensitivity of the PCR for detection of eae-positive E. coli andC. rodentium was between 1 and 2 CFU. To detect these sequences directly from sections of fixed colon from human and veterinary sources, PCR conditions were modified by the addition of 0.1 mM 8-methoxypsoralen to eliminate extraneous bacterial DNA from the PCR amplification cocktail without added template. Sections of colon from three pigs experimentally affected with colon lesions due to enteropathogenic (attaching and effacing) E. coli were PCR positive for bacterial eae genome. Sections from control animals were negative. Sections of colon from one of 18 biopsies from confirmed AIDS patients and from 22 of 35 colorectal cancer patients were PCR positive for bacterial eae genome. The PCR test was a simple and quick method of detecting bacterial eaegenome in human and veterinary clinical specimens. This method may remove the need for initial culture and detection of the gene by DNA probing from potential associated lesions. The clear relationship of bacteria containing the eae gene with colonic lesions in the pigs and mice indicates that a similar relationship is possible for human patients having similar lesions.

scholarly journals Sequence Variation in the E2-Binding Domain of HPV16 and Biological Function Evaluation in Tunisian Cervical Cancers

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Saloua Kahla ◽  
Lotfi Kochbati ◽  
Samia Hammami ◽  
Mohamed Badis Chanoufi ◽  
Mongi Maalej ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Variation ◽  
Expression Patterns ◽  
Pcr Amplification ◽  
Function Evaluation ◽  
Alternative Mechanism ◽  
Specific Sequence ◽  
Hpv16 E6 ◽  
E2 Gene ◽  
E6 And E7

HPV16 E2 variants have different effects on the transcriptional activity of the LCR. In this study, we examined the nucleotide and amino acid sequence variation within the HPV16 E2 gene and to correlate with disease progression. E2 gene disruption was detected by PCR amplification of the entire E2 gene using a single set of primers. Nucleotide variations were analyzed by bidirectional sequencing. mRNA expression patterns of E6 and E7 gene transcripts were evaluated by a reverse transcriptase-PCR method (RT-PCR). The detection of intact E2 genes was significantly higher among controls than cases (81.8% versus 37.5%, resp.,P<0.05). Among the E subgroup, variation at position 3684 C>A results in the amino acid substitution T310K and was more common among the E2 undisrupted cases (7/9; 77.7%), compared to controls (2/9; 22.2%). In addition, specific sequence variations identified in the E2 ORF at positions 3684 C>A were associated with increased viral oncogenes E6-E7 production. Besides HPV16 E2 disruption, the 3684 C>A variation within undisrupted E2 genes could be involved in an alternative mechanism for deregulating the expression of the HPV16 E6 and E7 oncogenes and appears to be a major factor contributing to the development of cervical cancer in Tunisian women.

Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene

Parasitology ◽  
2004 ◽  
Vol 129 (5) ◽  
pp. 537-547 ◽  
Author(s):  
S. J. WESTENBERGER ◽  
N. R. STURM ◽  
D. YANEGA ◽  
S. A. PODLIPAEV ◽  
R. ZELEDÓN ◽  
...  
Keyword(s):  
Costa Rica ◽  
Pcr Amplification ◽  
Gut Contents ◽  
Preliminary Survey ◽  
New Genera ◽  
Buffer Solution ◽  
Spliced Leader ◽  
Field Samples ◽  
Culture Independent ◽  
A Minor

The biodiversity of insect trypanosomes is largely unknown, resulting in significant gaps in the understanding of pathogen evolution. A culture-independent preliminary survey of trypanosomatid fauna was conducted for the parasites of Heteroptera (Hemiptera) from several localities in Costa Rica. Trypanosomatid infections were detected by light microscopy of smeared gut contents. Out of 257 insects representing 6 families, infections were found in 62 cases; cultures were obtained for 29 new isolates. Gut material from infected hosts was preserved in the field using an SDS–EDTA buffer solution for subsequent DNA extraction in the laboratory. PCR amplification of the trypanosomatid-specific spliced leader (SL) RNA gene repeats was successful for 60 field samples. Eighteen distinct SL RNA typing units were identified in a set of 28 samples analysed in detail. Cluster analysis indicated that these typing units were unique and thus could represent new species and, in some cases, new genera. This study reveals only a minor fraction of the trypanosomatid biodiversity, which is anticipated to be high.

DNA comparisons of Trypanosoma evansi (Indonesia) and Trypanosoma brucei spp.

Parasitology ◽  
1992 ◽  
Vol 104 (1) ◽  
pp. 67-74 ◽  
Author(s):  
W. T. Artama ◽  
M. W. Agey ◽  
J. E. Donelson
Keyword(s):  
Trypanosoma Brucei ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Consensus Sequence ◽  
Pcr Amplification ◽  
Trypanosoma Evansi ◽  
Base Pairs ◽  
Spliced Leader ◽  
Polymerase Chain ◽  
Minicircle Sequence

SUMMARYTwo clones from separate isolates of Trypanosoma evansi in Indonesia were found by polymerase chain reaction (PCR) analyses to contain 3 different repeated nuclear DNA sequences of Trypanosoma brucei spp: the consensus sequence for a highly repetitive 177 base pairs and the gene repeats encoding procyclin and the spliced leader. In addition, the 994 bp minicircle sequence of one of the clones was determined, and PCR amplification primers specific for minicircles of T. evansi were identified that do not amplify minicircle sequences in the T. brucei spp. clones tested.

Trypanosoma vivax: Characterization of the Spliced-Leader Gene of a Brazilian Stock and Species-Specific Detection by PCR Amplification of an Intergenic Spacer Sequence

2001 ◽  
Vol 99 (1) ◽  
pp. 37-48 ◽  
Author(s):  
Rogéria M Ventura ◽  
Fernando Paiva ◽  
Roberto A.M.S Silva ◽  
Gentilda F Takeda ◽  
Gregory A Buck ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Trypanosoma Vivax ◽  
Specific Detection ◽  
Spliced Leader ◽  
Species Specific
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