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At least 847 records · Page 47Linked to original sources
PubMed2005

[Random amplified polymorphic DNA analysis of tomato from seeds carried in Russian Mir space station].

OBJECTIVE: To identify the variation of hereditary substance of tomato offspring from seeds under long-duration spaceflight condition. METHOD: The tomato seeds carried in Russian MIR space station for six years, and the ground-based control were planted on the ground. The leaves of plants were used to do random amplified polymorphic DNA (RAPD) analysis. RESULT: Forty random primers were used in this study, among which 31 primers generated the same DNA band type, and 9 primers generated different DNA band types. Forty primers amplified 269 DNA bands, among which 29 DNA bands were polymorphic ones with a percentage of polymorphism of 10.8%. Compared with the control, plants from seeds carried in space station generated different band types. Band types were different among five plants from seeds carried in space station. The number of polymorphic bands generated by plant No. 5 compared with the control was the most, and that by plant No. 2 was the least. CONCLUSION: Long-duration spaceflight can cause variation of hereditary substance DNA of tomato.

DNA, Plant↗
PubMed1999

Pulsed-field gel electrophoresis is more efficient than ribotyping and random amplified polymorphic DNA analysis in discrimination of Pasteurella haemolytica strains.

One hundred thirty-three strains of Pasteurella haemolytica of both biotypes (90 and 43 strains of biotypes A and T, respectively) and almost all the serotypes were subjected to ribotyping, random amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE) analysis for epidemiological purposes. A total of 15 patterns recorded as ribotypes HA to HO were found for the P. haemolytica biotype A strains, with ribotypes HA, HC, and HD being encountered most often (66 strains [74%]); and 20 ribotypes, designated HA' to HT', that were clearly distinct from those observed for biotype A strains were observed for strains of biotype T. RAPD analysis generated a total of 44 (designated Rp1 to Rp44) and 15 (designated Rp1' to Rp 15') unique RAPD patterns for biogroup A and biogroup T, respectively. Analysis of the data indicated that a given combined ribotype-RAPD pattern could be observed for biotype A strains of different serotypes, whatever the zoological or geographic origin, whereas this was not the case for biotype T strains. PFGE appeared to be more efficient in strain discrimination since selected strains from various zoological or geographical origins harboring the same ribotype-RAPD group were further separated into unique entities.

Animals↗
PubMed2002

Ultra-rapid DNA analysis using HyBeacon probes and direct PCR amplification from saliva.

We describe a novel probe technology, termed HyBeacons, which provides a new homogeneous method for fluorescence-based sequence detection and allele discrimination. Employing a single nucleotide polymorphism located in the N-acetyltransferase 2 gene as a model system, we demonstrate the utility of HyBeacon probes for rapid and reliable sequence analysis. We also demonstrate that homozygous and heterozygous samples may be accurately identified using a single HyBeacon oligonucleotide. Polymorphic DNA sequences were detected and differentiated by real-time PCR and melt peak methodologies, without performing extraction of genomic DNA prior to target amplification. Employing a combination of homogeneous HyBeacon analysis, the rapid thermal cycling conditions of the LightCycler and direct amplification from saliva, allowed samples to be genotyped within 30 min. Such rapid non-invasive diagnostic technologies may permit 'point-of-care' genetic testing to be performed in hospitals and doctor's surgeries.

Arylamine N-Acetyltransferase↗
PubMed1999

Comparison of ribotyping, randomly amplified polymorphic DNA analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains.

A total of 24 strains, biochemically identified as members of the Lactobacillus casei group, were identified by PCR with species-specific primers. The same set of strains was typed by randomly amplified polymorphic DNA (RAPD) analysis, ribotyping, and pulsed-field gel electrophoresis (PFGE) in order to compare the discriminatory power of the methods. Species-specific primers for L. rhamnosus and L. casei identified the type strain L. rhamnosus ATCC 7469 and the neotype strain L. casei ATCC 334, respectively, but did not give any signal with the recently revived species L. zeae, which contains the type strain ATCC 15820 and the strain ATCC 393, which was previously classified as L. casei. Our results are in accordance with the suggested new classification of the L. casei group. Altogether, 21 of the 24 strains studied were identified with the species-specific primers. In strain typing, PFGE was the most discriminatory method, revealing 17 genotypes for the 24 strains studied. Ribotyping and RAPD analysis yielded 15 and 12 genotypes, respectively.

Bacterial Typing Techniques↗
PubMed1996

Flow cytometric DNA analysis of gastric cancer that is invading the muscularis propria.

OBJECTIVE: To find out if there is any correlation between the DNA aneuploidy in gastric cancer that is invading the muscularis propria and survival. DESIGN: Retrospective study. SETTING: Teaching hospital, Japan. SUBJECTS: 52 patients who underwent gastric resection for gastric cancer that was invading the muscularis propria, and for whom clinical follow-up data were available. INTERVENTIONS: Flow cytometric measurement of DNA in paraffin-embedded tissue. MAIN OUTCOME MEASURES: Correlation between survival and clinicopathological variables including ploidy. RESULTS: 22 (42%) of the cases were aneuploid and 30 (58%) were diploid. The lymph node status and DNA ploidy were the significant prognostic variables, but a multivariate analysis showed that only DNA ploidy was significant. CONCLUSIONS: Nuclear DNA ploidy is an independent prognostic factor in gastric cancer that is invading the muscularis propria.

Aneuploidy↗
PubMed2001

Mitochondrial DNA analysis in the Turkish Leber's hereditary optic neuropathy population.

PURPOSE: To define the prevalence of a panel of mitochondrial DNA (mtDNA) mutations associated with Leber's hereditary optic neuropathy (LHON) in the Turkish LHON population. LHON-associated mtDNA mutations have been found in LHON patients from around the world, but the Turkish LHON population has not been studied. METHODS: Thirty-two Turkish patients were defined clinically as having LHON on the basis of painless, subacute, bilateral optic neuropathy and the exclusion of other causes of subacute optic neuropathy. mtDNA was extracted from blood of the 32 probands and assayed for a panel of primary and secondary LHON-associated mtDNA mutations by polymerase chain reaction (PCR)-based methods. We studied three well-known LHON-associated primary mutations (at nucleotide positions 11778, 3460 and 14484) and one common secondary mutation (at nucleotide 15257) in all 32 probands. In addition to these mutations, 18 of the 32 probands were tested for the Complex IV, COX III gene, LHON associated 9804 and 9438 mutations and secondary LHON mutations at nucleotide positions 3394, 4160, 4216, 4917, 5244, 7444, 7706, 13708, 13730 and 15812. RESULTS: Among the 32 probands tested for four common LHON mutations, 3 carried the 14484 mutation, 1 carried the 11778 mutation, 1 carried the 3460 mutation and 1 carried the 15257 mutation. Among the 18 LHON patients who tested for additional mutations, 1 proband harboured the 9804 mutation and 4 carried the secondary mutations at nucleotide positions 4216, 4917 and 13708. CONCLUSION: The results of mtDNA analysis of the Turkish LHON patients appear to be different from those of previous reports.

Adolescent↗
PubMed1981

Molecular cloning of equine herpesvirus type 1 DNA: analysis of standard and defective viral genomes and viral sequences in oncogenically transformed cells.

Genomic DNA sequences of equine herpesvirus type 1 (EHV-1) have been cloned as BamHI and EcoRI restriction fragments into the plasmid pBR322 and propagated in Escherichia coli. With the exception of two EcoRI restriction fragments that reside in the S region of the viral genome, all of the cloned fragments demonstrated the same electrophoretic mobilities, restriction cleavage sites, and blot-hybridization patterns as did the parent fragments produced by BamHI or EcoRI digestion of virion DNA. The EcoRI J fragment and the BamHI E fragment of the L-region terminus were cloned after the addition of appropriate linker oligonucleotides. Fragments originating from each of the two isomeric forms of EHV-1 DNA were contained in this library of clones. Supramolar DNA fragments present only in the DNA of defective interfering (DI) particles of EHV-1 were generated from Bgl II digestion of DNA preparations enriched for EHV-1 DI particles and were cloned as Bgl II and EcoRI fragments into the plasmid vector. The cloned viral sequences represented in this defective genome mapped to the S region of EHV-1 DNA. Blot-hybridization analysis of EHV-1 transformed and tumor cell DNAs with the cloned BamHI B fragment confirmed that subgenomic viral sequences are present and indicated that those sequences map to the viral genome between 0.32 and 0.43 map unit.

Animals↗
PubMed2001

Genetic diversity and molecular markers of cupped oysters (genera Crassostrea, Caccostrea, and Striostrea) in Thailand revealed by randomly amplified polymorphic DNA analysis.

Genetic diversity and species-diagnostic markers of 5 oysters in Thailand, Crassostrea belcheri (Sowerby, 1871), Crassostrea iredalei (Faustino, 1932), Saccostrea cucullata (Born, 1778), Saccostrea forskali (Gmelin, 1791), and Striostrea Parastriostrea) mytiloides (Lamarck, 1819), were investigated by randomly amplified polymorphic DNA (RAPD) analysis. In a total, 135, 127, and 108 genotypes were observed from primers OPA09, OPB01, and OPB08 (Operon Technologies Inc., kits A and B), and 131 and 122 genotypes from primers UBC210 and UBC220 (University of British Columbia), respectively. Two hundred fifty-four reproducible and polymorphic fragments (200-2500 bp in length) were generated across the 5 investigated species. The average number of bands per primer varied between 12.4 and 32.2. The percentage of polymorphic bands within Crassostrea (53.23%-77.67%) was lower than that within Saccostrea and Striostrea oysters (86.21%-99.36%). Nine, species-specific markers were found in C. belcheri, 4 in C. iredalei, and 2 in S. cucullata. The mean of a ratio between the number of genotypes generated by each primer and the number of investigated specimens of C. belcheri (0.58) was lower than that of the remaining species (0.90-1.00). Genetic distances between pairs of oyster samples were between 0.105 and 0.811. A neighbor-joining tree indicated distant relationships between Crassostrea and Saccostrea oysters, but closer relationships were observed between the latter and Striostrea mytiloides.

Journal Article↗
PubMed1989

The relationship of flow cytometric DNA analysis and clinicopathology in small-intestinal carcinoids.

Paraffin-embedded archival tissue samples were used for nuclear deoxyribonucleic acid (DNA) content study by flow cytometry on 56 surgically resected, primary, small-intestinal carcinoid tumors. Sample preparation was carried out using the methods of Hedley and Vindelov. To reduce nuclear aggregation, a procedure of sonication was also performed. Nineteen (34%) cases were DNA diploid, 34 (61%) cases showed significantly increased 4C peak (DNA tetraploid), and only three (5%) cases were DNA aneuploid. Cell cycle phase analysis revealed that carcinoid tumors had significantly higher G2% than those of nontumor control tumors. However, there was no significant correlation between clinical parameters and both DNA ploidy pattern and cell cycle phase analysis. Although the difference in survival between patients with DNA nondiploid tumors and DNA diploid tumors was not significant, all of the patients with DNA aneuploid tumor had poor prognosis followed by death from carcinoid tumor.

Adult↗
PubMed1990

HLA class II genes: typing by DNA analysis.

A detailed understanding of the structure and function of the human major histocompatibility complex (MHC) has ensued from studies by molecular biologist during the last decade. Virtually all of the HLA genes have now been cloned, and the nucleotide sequences of their different allelic forms have been determined. Typing for these HLA alleles is a fundamental prerequisite for tissue matching in allogeneic organ transplantation. Until very recently, typing procedures have been dominated by serological and cellular methods. The availability of cloned DNA from HLA genes has now permitted the technique of restriction fragment length polymorphism (RFLP) analysis to be applied, with remarkable success and advantage, to phenotyping of both HLA Class I and Class II determinants. For the HLA Class II genes DR and DQ, a simple two-stage RFLP analysis permits the accurate identification of all specificities defined by serology, and of many which are defined by cellular typing. At the present time, however, RFLP typing of HLA Class I genes is not as practicable or as informative as that for HLA Class II genes. The present clinical applications of HLA-DR and DQ RFLP typing are predominantly in phenotyping of living donors, including selection of HLA-matched volunteer bone marrow donors, in allograft survival studies, and in studies of HLA Class II-associated diseases. However, the time taken to perform RFLP analysis precludes its use for the typing of cadaveric kidney donors. Nucleotide sequence data for the alleles of HLA Class II genes have now permitted the development of allele-specific oligonucleotide (ASO) typing, a second category of DNA analysis. This has been greatly facilitated by the ability to amplify specific HLA Class II DNA 'target' sequences using the polymerase chain reaction (PCR) technique. The accuracy of DNA typing techniques should ensure that this methodology will eventually replace conventional HLA phenotyping.

DNA↗
PubMed1991

Identification of the skeletal remains of a murder victim by DNA analysis.

There is considerable anthropological and forensic interest in the possibility of DNA typing skeletal remains. Trace amounts of DNA can be recovered even from 5,500-year-old bones and multicopy human mitochondrial DNA sequences can frequently be amplified from such DNA using the polymerase chain reaction (PCR). But given the sensitivity of PCR, it is very difficult to exclude contaminating material. We now report the successful identification of the 8-year-old skeletal remains of a murder victim, by comparative typing of nuclear microsatellite markers in the remains and in the presumptive parents of the victim. This analysis establishes the authenticity of the bone DNA and the feasibility of bone DNA typing in forensic investigations.

Adolescent↗
PubMed1988

DNA analysis of hepatocellular carcinoma and clinicopathologic implications.

Cell nuclear DNA content was microspectrophotometrically measured in 60 specimens of clinical hepatocellular carcinoma (HCC). The DNA distribution pattern was classified into two types, diploid and nondiploid, according to the degree of dispersion on the DNA histogram. Among these 60 specimens, 26 had an HCC of less than 5 cm in diameter. In these 26, 17 (65%) had the diploid pattern and 9 (35%) had the nondiploid pattern. In the remaining 34 specimens with a large HCC exceeding 5 cm in diameter, the diploid pattern was seen in only six (18%), and the nondiploid pattern was seen in 28 (82%). Following increase in tumor size, the number of cases of nondiploid increased. The DNA pattern closely correlated with the morphologic grading and age of patients, yet there was no correlation among DNA pattern and presence of hepatitis B surface antigen (HBsAg) or presence of liver cirrhosis. Regarding the prognosis of patients with HCC, there was no statistic difference between DNA pattern and prognosis. The present study suggests that the DNA pattern relates to the biologic characteristics of the growth pattern of HCC. However, the DNA pattern showed no significant correlation with survival rates of patients with HCC who underwent hepatic resection.

Adult↗
PubMed1993

Flow cytometric DNA analysis of wheat-rye addition lines.

The nuclear DNA content of the 7 wheat-rye chromosome addition lines were determined by flow cytometry. The nuclear DNA content of each line was compared to the original wheat parental line. From this information, the amount of DNA per rye chromosome was calculated. The DNA per chromosome ranged from 0.8 picograms (pg) in chromosome 3R to 1.4 pg in chromosome 7R. Flow cytometry was proven to be a rapid and reliable technique for the evaluation of aneuploid plant populations. Flow cytometry has the potential to allow for more rapid screening of aneuploid and euploid cytological stocks than conventional cytogenetic techniques.

Aneuploidy↗
PubMed1994

Flow cytometric DNA analysis of colorectal carcinoid.

We analyzed the patterns of DNA ploidy in 31 colorectal carcinoid tumors from paraffin-embedded tissues by DNA flow cytometry and the relationship of the patterns of DNA ploidy to prognosis. Diploid DNA was found in 78% (24 of 31) of carcinoids and tetraploid in 6% (2 of 31). Five (16%) carcinoids were DNA aneuploid, and four of the patients with aneuploidy showing a near-hypertriploid pattern died during the first 5 years of follow-up. The association of aneuploidy with stage, size, and invasion of tumor was significant. However, our data indicated that DNA aneuploidy of a near-hypertriploid pattern was the most precise and reliable parameter for predicting the prognosis of colorectal carcinoid tumors.

Adult↗
PubMed1999

Mitochondrial DNA analysis of Sporothrix schenckii clinical isolates from China.

Mitochondrial DNA (mtDNA) types based on restriction fragment length polymorphism (RFLP) patterns with HaeIII were investigated in clinical isolates of Sporothrix schenckii in China. In addition to 23 mtDNA types (Types 1-23) so far reported, a new mtDNA type (Type 24) was found in this study. Type 24 was divided into two subtypes, Subtype 24A and 24B based on RFLP with EcoRV. Sixty-seven isolates in China consisted of 58 isolates of Type 4, 5 of Type 6, 1 of Type 5, 1 of Type 20 and 2 of Type 24. Based on the phylogeny of the mtDNA types (Types 1-24) constructed by estimating sequence divergences of mtDNA, mtDNA types clustered into two groups: Group A (Types 1-3, Type 11, Types 14-19 and Types 22-23) and Group B (Types 4-10, Types 12-13, Types 20-21 and Type 24). These results suggest that most S. schenckii isolates in China belong to Group B.

China↗
PubMed1991

Cytogenetic and flow cytometric DNA analysis in renal cell carcinoma.

Cytogenetic and flow cytometric DNA analyses were performed on 37 tumor samples from 16 patients with renal cell carcinoma. 36 cultures were chromosomally abnormal and 1 was normal. The most frequent abnormality was trisomy or tetrasomy of chromosome 7 (13 of 16 tumors), suggesting that this abnormality might be a primary change in renal cell carcinoma. Abnormalities of chromosome 3 were seen in 9 of 16 tumors (56%). Eight of 11 tumors (73%) with cytogenetic results from multiple tumor samples showed intratumor cytogenetic heterogeneity. Twelve of the 16 patients had aneuploid tumors, and 4 had homogeneously diploid tumors. DNA index correlated with chromosome number. No association was found between cytogenetic results and clinical stage.

Aneuploidy↗
PubMed1994

[Flow cytometric DNA analysis of colorectal carcinoma in adenoma].

We evaluated the DNA ploidy in 23 lesions of colorectal carcinoma in adenoma (CIA) and 90 adenomas without carcinomas by flow cytometry using fresh samples. DNA ploidy of carcinoma and adenoma components were assessed, respectively, with 17 paraffin-embedded samples of CIAs. The incidence of DNA aneuploidy (AP) was significantly higher in CIAs than in adenomas (47.8% vs. 12.2%, p < 0.01). Even in adenoma components of CIAs, AP tended to be found more frequent than in adenomas (41.2% vs. 12.2%). The incidence of AP in adenoma components was similar to that in carcinoma components (35.3%) in CIAs. In conclusion, DNA aneuploidy in adenomas may be a marker of malignant potential.

Adenoma↗