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At least 433 records · Page 24Linked to original sources
PubMed1982

Differentiation of subtypes within Leptospira interrogans serovars Hardjo, Balcanica and Tarassovi, by bacterial restriction-endonuclease DNA analysis (BRENDA).

Various strains of Leptospira interrogans were compared by bacterial restriction-endonuclease DNA analysis (BRENDA). Field strains of serovar hardjo isolated from domestic animals in New Zealand, Australia and Northern Ireland were indistinguishable from one another but differed strikingly from the hardjo reference strain Hardjoprajitno. Similarly, field isolates of balcanica and tarassovi differed from their serovar reference strains, probably owing to a difference in epidemiological niche. Subdivision of these serovars into distinct subtypes as defined by BRENDA is therefore useful and justified. In contrast, analysis of serovars pomona, ballum and copenhageni shows that field and reference strains were identical, or differed only by a single band. It is suggested that BRENDA will overcome many of the problems associated with serological methods of identifying serovars and allow more precise definition of epidemiological relationships between strains and their hosts.

Base Sequence↗
PubMed1992

Phylogenetic relationships of the genera Arthroderma and Nannizzia inferred from mitochondrial DNA analysis.

The phylogenetic relationship of the genera Arthroderma and Nannizzia, was investigated by mitochondrial DNA analysis based on the restriction-fragment-length polymorphisms. Phylogenetic trees made on ten species. A. benhamiae, A. insingulare, A. quadrifidum, A. simii, A. vanbreuseghemii, N. fulva, N. grubyia, N. gypsea, N. incurvata and N. otae showed no definite distinctions between the genera Arthroderma and Nannizzia. These results support the conclusion of Weitzman et al. that the genera Arthroderma and Nannizzia are congeneric.

Ascomycota↗
PubMed1994

DNA analysis by flow cytometry of paraffin embedded core biopsies of the prostate.

The majority of literature concerning DNA analysis of prostate cancer involves testing formalin-fixed prostatectomy tissue, fresh or formalin-fixed transurethral resections of the prostate (TURP), or fresh core biopsies. We were interested if flow cytometry could analyze the DNA of formalin-fixed, paraffin-embedded, core biopsies separated into normal versus malignant segments. Of the 50 potentially available samples for analysis representing 11 controls of normal core tissue and 39 core biopsies from the 11 patients, one patient had no normal tissue, one core had no malignancy, and three cores had no tissue visibly remaining in the paraffin blocks for analysis. Therefore, of 45 actual samples available for processing, sometimes representing segments as small as 0.2 cm, separate segments containing malignant glands or normal glands were excised from the blocks, and processed separately by the Hedley technique. Forty-four of the 45 available samples produced interpretable DNA histograms as defined by discernible G0/G1 peaks, a calculable cell cycle analysis, and the qualitative appearance of a "smooth" histogram appearance, reflecting sufficient nuclei were analyzed. This is the first report to our knowledge where flow cytometry has successfully been used to analyze paraffin blocks of core biopsies which were, in addition, separated into malignant versus normal enriched segments.

Biopsy↗
PubMed1989

[Diagnosis by DNA analysis in familial isolated growth hormone deficiency type I-A].

We show the autoradiograms of DNA from one child affected of familial isolated growth hormone deficiency type I-A. Restriction endonuclease analysis of DNA isolated from leukocytes was done using 32P-labeled human GH cDNA clone as a probe. DNA analysis using the restriction endonuclease Bam HI revealed that the 3.8 kb restriction fragment, which contain the normal hGH-N gene, was absent. Since these deletions preclude production of any GH-N protein, affected individuals tend to be immunologically intolerant to exogenous GH. The child was homozygote and after treatment with exogenous GH developed a high titre of antibodies to GH and growth arrest. This is the first case of this genetic disorder studied in Spain.

Autoradiography↗
PubMed1999

Genomic instability in silica- and cadmium chloride-transformed BALB/c-3T3 and tumor cell lines by random amplified polymorphic DNA analysis.

Our earlier studies using random amplified polymorphic DNA (RAPD) analysis have shown genetic instability in human lung cancer tissues. Here we have investigated the potential for genetic instability in silica- and cadmium chloride (CdCl2)-transformed BALB/c-3T3 cell lines. Non-transformed, transformed BALB/c-3T3 cells, and tumor cell lines (obtained by injecting nude mice with transformed cell lines) were analyzed for genomic changes. DNAs from 10 different transformed clones and their corresponding tumor cell lines were amplified individually by RAPD analysis using 10 arbitrary primers. DNA from non-transformed BALB/c-3T3 cells was used as a control to compare genetic alterations, if any, between non-transformed, transformed and tumor cell populations. PCR products from RAPD were electrophoretically separated on agarose gels and the banding profiles were visualized by ethidium bromide staining. Five of the 10 primers tested revealed genomic changes in silica-transformed cell lines when compared to non-transformed BALB/c-3T3 cells. Comparison of all 10 transformed and tumor cell lines showed varied degrees of genomic changes using all 10 primers. CdCl2-transformed cell lines displayed fewer genomic changes, only three of 10 primers showed a positive result. CdCl2-transformed cells and their corresponding tumor cell lines showed specific banding pattern differences in six of the 10 samples tested with six of the 10 primers. Changes in band intensity were the most commonly observed changes both in silica- and CdCl2-transformed and tumor cell lines. The results seem to indicate a progressive change in genomic rearrangements which may directly or indirectly be associated with progression of tumorigenesis.

3T3 Cells↗
PubMed1988

Flow cytometric DNA analysis of medulloblastoma. Prognostic implication of aneuploidy.

Paraffin-embedded surgical specimens from 26 infants and children with medulloblastomas treated between 1972 and 1981 were examined for DNA ploidy by flow cytometry (FCM). All patients received a standard treatment (a combination of maximum debulking of medulloblastoma and postoperative craniospinal irradiation with a posterior fossa boost of 5000 rad or more). They were studied to correlate the results of the findings of FCM DNA analysis with their final outcome, DNA ploidy, and extent of tumor resection. All seven patients with totally resected aneuploid medulloblastoma are alive, whereas only one of six patients with subtotally resected diploid medulloblastoma is alive (P = 0.0047). The current study suggests both DNA ploidy and extent of surgical resection are the most important determinant of patients' prognosis. Patients in selected group, particularly those with subtotally resected diploid tumor, are advised to undergo aggressive adjuvant chemotherapy.

Adolescent↗
PubMed1992

Flow-cytometric DNA analysis of stages IB and IIA cervical carcinoma.

The prognostic significance of flow-cytometric DNA analysis was assessed in 375 stages IB and IIA squamous cell carcinoma patients treated with radical hysterectomy and lymphadenectomy at the Mayo Clinic between 1956 and 1985. Paraffin-embedded samples containing at least 20% tumor were dewaxed, rehydrated, stained with propidium iodide, and analyzed. Among 344 assessable samples, 136 (40%) were diploid and 208 (60%) were nondiploid (26 tetraploid, 158 aneuploid, and 24 polyploid). Diploid cases were further subclassified: 25 high proliferative phase (HPP) (S+G2M greater than 20%) and 111 low proliferative phase. No significant correlation was noted between DNA diploid patterns and stage, tumor size, grade, or histotype, but HPP diploid tumors had a significantly higher risk of nodal metastasis. With a mean follow-up period of 150 months, 62 patients died of disease. No significant difference was observed in survival rates (SR) between diploid and nondiploid tumors, but the subset of HPP diploid tumors had a prognosis significantly worse than that of any other group (P less than 0.01). Other significant variables included nodal metastases, parametrial extension, age, and clinical stage. While ploidy patterns did not assign additional risk to node-positive lesions, HPP diploid tumors in node-negative patients were associated with a significantly lower SR. Multivariate analyses in node-negative patients demonstrated that stage, histologic subtype, and HPP diploid patterns retained prognostic independence.

Carcinoma, Squamous Cell↗
PubMed1998

Flow cytometric DNA analysis with cytokeratin gating of formalin-fixed deparaffinized breast cancer nuclei.

The "gold standard" inflow cytometric DNA analysis of breast cancer uses fresh tumor cells simultaneously labeled for cytokeratin (CK) and DNA. We developed a 2-parameter CK-DNA flow assay suitable for archival, paraffin-embedded tissue (PT). Six anti-CK monoclonal antibodies were tested by immunocytochemistry and our assay for staining of nuclei extracted from PT breast cancers by combination pepsin-trypsin digestion. Clone CAM 5.2 was inadequate for PT nuclear suspensions, but a cocktail of 2 anti-CK clones (AE1/AE3 and KL-1) distinguished epithelial from nonepithelial nuclei in 2-parameter flow dot plots. We studied 82 routine PT breast tumors by our assay and used a univariate flow DNA histogram based on fresh biopsy tissue for comparison. Three histogram data quality indicators were improved. A trend toward higher S-phase fractions was found for DNA diploid PT tumors, although when inflammation was evident histologically, the increment in S-phase fraction with gating was often marked. CK gating identified PT tumors containing concurrent CK-positive DNA diploid and nondiploid populations (27 of 56 DNA nondiploid histograms). By excluding nonepithelial nuclei, 2-color CK-DNA flow methods may increase the accuracy of ploidy and S-phase fraction measurements. Our method appears superior to previous techniques using clone CAM 5.2 for labeling of archival breast cancers.

Antibodies, Monoclonal↗
PubMed1997

Automated image analysis DNA cytometry to predict the pathological stage in clinical stage I nonseminomatous testicular germ cell tumors.

OBJECTIVE: Automated image analysis DNA cytometry was used to predict the pathological stage in clinical stage I nonseminomatous testicular germ cell tumor patients. METHODS: Orchiectomy specimens of 74 patients (41 pathological stage I, 33 pathological stage II) were analyzed by modular image analysis computer, and several mathematical indices from the DNA histogram were calculated. RESULTS: The 5c-exceeding rate (rate of hyperpentaploid nuclei) was found to be significantly higher in patients with pathological stage II disease as compared with patients without metastases (p = 0.0174). Tumor tissue from lymph node metastases showed even higher amounts of hyperpentaploid nuclei (p < 0.0005). In this study, all patients with a 5c-exceeding rate above 3.1% had metastatic disease. CONCLUSIONS: Single-cell cytophotometry was able to show significant differences in 5c-exceeding rates between patients with and without tumor metastases. Because of high standard deviations, however, it was not possible to use this parameter for correct staging in all patients.

Analysis of Variance↗
PubMed2001

Diagnosis of alpha-1-antitrypsin deficiency by DNA analysis of children with liver disease.

BACKGROUND: Alpha-1-antitrypsin deficiency is a genetic disorder which is transmitted in a co-dominant, autosomal form. Alpha-1-antitrypsin deficiency affects mainly the lungs and the liver leading, in the latter case, to neonatal cholestasis, chronic hepatitis or cirrhosis. A precise diagnosis of Alpha-1-antitrypsin deficiency may be obtained by biochemical or molecular analysis. OBJECTIVE: The purpose of this study was to use DNA analysis to examine the presence of an alpha-1-antitrypsin deficiency in 12 children suspected of having this deficiency and who showed laboratory and clinical characteristics of the disease. PATIENTS AND METHODS: Twelve patients, aged 3 months to 19 years, who had serum alpha-1-antitrypsin levels lower than normal and/or had hepatic disease of undefined etiology were studied. The mutant alleles S and Z of the alpha-1-antitrypsin gene were investigated in the 12 children. Alpha-1-antitrypsin gene organization was analyzed by amplification of genome through the polymerase chain reaction and digestion with the restriction enzymes Xmnl (S allele) and Taq-1 (Z allele). RESULTS: Seven of the 12 patients had chronic liver disease of undefined etiology and the other five patients had low serum levels of alpha-1-antitrypsin as well as a diagnosis of neonatal cholestasis and/or chronic liver disease of undefined etiology. Five of the 12 patients were homozygous for the Z allele (ZZ) and two had the S allele with another allele (*S) different from Z. CONCLUSION: These results show that alpha-1-antitrypsin deficiency is relatively frequent in children with chronic hepatic disease of undefined etiology and/or low alpha-1-antitrypsin levels (41.6%). A correct diagnosis is important for effective clinical follow-up and for genetic counseling.

Adolescent↗
PubMed1986

DNA analysis in human disease.

The analysis of human DNA using recombinant DNA technology is fast becoming an integral part of the diagnosis, assessment, and prevention of inherited and somatic genetic disease. The rationale underlying these methods of analysis is discussed, and the nature and extent of mutational change in heritable disorders and neoplastic development is outlined.

DNA↗
PubMed1995

Randomly amplified polymorphic DNA analysis of Xylella fastidiosa Pierce's disease and oak leaf scorch pathotypes.

Randomly amplified polymorphic DNA analysis was conducted with 14 primers to 17 strains of Xylella fastidiosa. There was a high degree of similarity among the seven Pierce's disease (PD) strains (Sxy > 0.93) and the seven oak leaf scorch (OLS) strains (Sxy > 0.96). However, the two groups were different, with a similarity index of 0.67, confirming the presence of a PD DNA cluster and suggesting the presence of a new OLS cluster. The control plum leaf scald strains (two strains) together with the periwinkle wilt strain had a much smaller similarity index (0.44) compared with the PD and OLS clusters.

Base Sequence↗
PubMed2004

Ninhydrin treatment as a screening method for the suitability of swabs taken from contact stains for DNA analysis.

More and more swabs containing unknown traces of biological material are submitted for forensic DNA analysis. Most of the samples are swabs taken from handled items such as tools, weapons and handles etc. Therefore, we tried to develop a screening method in order to focus the investigation on samples containing biomolecules, such as amino acids which might be associated with nucleic acids. A total of 285 swabs taken from various items collected during crime scene investigations were treated with ninhydrin which leads to a purple colour for samples containing amino acids. Of the swabs 158 were classified as ninhydrin positive and 76% of these samples yielded DNA profiles that fulfil the criteria for inclusion in the German national DNA database (profile frequency greater than 1 in 100,000) or in DNA mixtures which could at least be compared with suspects. In comparison only 9% of the 127 samples shown to be ninhydrin negative, revealed a usable DNA profile. Consequently, ninhydrin treatment was found to be an effective screening method which resulted in an increase in the rate of successfully typed samples and subsequently in a reduction of the costs due to the lower number of samples that needed to be typed.

DNA Fingerprinting↗
PubMed1999

Population subdivision among desert bighorn sheep (Ovis canadensis) ewes revealed by mitochondrial DNA analysis.

We used behavioural observations and mitochondrial DNA (mtDNA) sequence analysis to examine demographic and genetic structure within and among home-range groups of desert bighorn sheep (Ovis canadensis) ewes in the Peninsular Ranges of southern California, USA. We identified substantial genetic variation in the first 515 bp of the mtDNA control region and determined that seven haplotypes were distributed in a nonrandom fashion among these ewe subpopulations. Although a significant (P < 0.01) amount of mtDNA variation (33%) was partitioned among home-range groups, we did not find strong evidence for matrilineal substructuring within these groups. Based on analyses of molecular variance, and comparisons of behavioural associations and distances between centres of activity, we concluded that within a given home-range group, bighorn sheep ewes generally associate with other ewes based on their availability rather than their matrilineal relationships. Our results also supported the conclusion that multiple ewe subpopulations exist within the Peninsular Ranges, and that these subpopulations are the most basic demographic and genetic units.

Animals↗
PubMed1997

[A case of juvenile Huntington's disease presenting dystonia and confirmed by DNA analysis].

We reported a 13-year-old boy with juvenile Huntington disease diagnosed by DNA analysis. Symptoms started with dysarthria at 6 years of age, which was followed by progressive dysgraphia and gait disturbance due to dystonia from 7 years, and by epileptic seizures from 12 years. Magnetic resonance imaging revealed atrophy of the bilateral caudate nuclei and T2- and proton-weighted high intensity area in both putamina. The CAG (cytosine-adenine-guanine) trinucleotide repeat on chromosome 4 p16 was markedly expanded to 81. For a child with dystonia with mental deterioration, juvenile Huntington disease should be considered in the differential diagnosis.

Adolescent↗
PubMed1999

Prenatal diagnosis of sporadic neurofibromatosis type 1 (NF1) by RNA and DNA analysis of a splicing mutation.

Neurofibromatosis type 1 (NF1) is one of the most common genetic disorders in humans with an incidence of 1 in 3500. Most of the NF1 mutations reported so far (over 240 mutations) are unique. Specific prenatal diagnosis can only be provided to familial cases by an indirect linkage analysis or to families with a previously identified mutation. Here we report the first prenatal diagnosis in sporadic NF1 by direct characterization of the mutation. We first identified the skipping of exon 10b of NF1 in the mRNA from a woman affected by NF1 and without familial history of the disease. The analysis of genomic DNA identified mutation IVS10b+1G-->A as the cause of the skipping of exon 10b. Chorionic villus sampling (CVS) was performed at 10 weeks of gestation and total RNA was directly extracted from the sample. After reverse transcription (RT) and polymerase chain reaction (PCR) of the cDNA, the skipping of exon 10b was not identified in the CVS upon agarose gel electrophoresis. The fetal origin of the CVS was confirmed via polymorphic markers and the absence of the IVS10b+1G-->A mutation was confirmed by genomic analysis.

Adult↗
PubMed1993

Microbial DNA challenge studies of variable number tandem repeat (VNTR) probes used for DNA profiling analysis.

DNA probes commonly used for forensic DNA profiling analysis were hybridized to Hinfl digested DNA isolated from various common microbial species. Extended exposures to light sensitive film failed to detect any DNA fragments of a microbial origin following hybridizations to radio-labeled DNA insert single-locus probes (SLPs) and nonisotopically labeled oligonucleotide SLPs.

DNA Fingerprinting↗
PubMed1990

[Diagnosis of multiple endocrine neoplasms type IIa using DNA analysis].

The gene causing MEN IIa has recently being assigned to the pericentromeric region of chromosome 10. We performed linkage analysis using DNA-markers closely related to the chromosomal locus at chromosome 10: MCK II, retinol binding protein cDNA and cTBIRBP-9. Available for the study were EDTA blood from two families. The analysis was positive in two asymptomatic offsprings in one family (B), whereas the markers were not informative in the other family (A). Genetic distance of the informative marker of family A to MEN IIa gene is 2 cM, i.e. a likelihood of 98% (95% up a confidence limit with 5%) for the gene carrier status of two children aged 11 and 7 y old. The following clinical investigation including pentagastrin test, plasma catecholamines and 24 hour urine catecholamines and parathormone was negative until now. We recommend early linkage analysis for establishing the genetic status in offspring of MEN IIa families to focus further screening to those, who are predicted to be gene carrier.

DNA, Neoplasm↗