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Rapid and simple diagnosis of the two common alpha 1-proteinase inhibitor deficiency alleles Pi*Z and Pi*S by DNA analysis.

We describe a simple DNA-based method to assign the two common alpha 1-proteinase inhibitor (alpha 1-antitrypsin) deficiency alleles in the Pi-system (Pi*Z and Pi*S). Two sets of mutated primers are used in the polymerase chain reaction (PCR), followed by a restriction enzyme digest of the products. The mutated forward primers create a Taq I site only if the wildtype alleles (mostly M or subtypes) are present and not in the presence of the Pi*Z or Pi*S alleles. The reverse primers are mutated for an invariant Taq I site which serves as an internal control site in order to assure the completion of the restriction enzyme digest. The digested PCR products can be clearly resolved by 2.5% MetaPhore-agarose gel electrophoresis. This simple PCR probing of the most common alpha 1-antiproteinase deficiency alleles can be routinely applied either to samples showing quantitatively decreased alpha 1-antiproteinase values in serum or to blood spots of Guthrie cards used for mass screening purposes. In addition, this method may provide the opportunity for a simple, rapid, and reliable prenatal diagnosis of alpha 1-antiproteinase deficiency in special cases.

Alleles↗

Retroactive DNA analysis for sex determination and dystrophin gene by polymerase chain reaction with archived cytogenetic slides.

We describe a rapid and efficient diagnostic method for sex determination and the dystrophin gene by the polymerase chain reaction (PCR) using archived cytogenetic slides. Archived cytogenetic slides stored for about 4 years at room temperature were used. To confirm whether DNA analysis is possible using the archived cytogenetic slides, we extracted the DNA from the slides and amplified the Y centromeric region (DYZ3), the X centromeric region (DXZ1) and the exon 46 of the dystrophin gene. Of the 50 cases, 24 were peripheral bloods, 13 were amniotic fluid cells, 5 were chorionic villus samplings and 8 were cord bloods. The PCR related sex determination in 22 females and 28 males, showed 100% concordance with the results of chromosome analysis, and all cases showed positive band for the exon 46 of the dystrophin gene. Of the 50 cases of the archived cytogenetic slides, we were fortunate enough to obtain the fresh blood sample from one fetus whose karyotype showed 45,X[34]/46,X,+mar[145] to compare the results of the gDNA with that from archived cytogenetic slide. To confirm whether the marker chromosome was derived from Y chromosome, we studied the six loci (PABY, SRY, RPS4Y (SY16, 17), ZFY, DYS14) on the short arm, one locus (DYZ3) on the centromere and one locus (DYZ1) on the long arm. Of the 8 loci studies, all PCR related Y chromosome showed positive band from both gDNA obtained from cord blood and archived cytogenetic slides. We could conclude from the above results that the marker chromosome was derived from the Y chromosome. We believe our experiment is rapid and efficient for studies of over 10 independent loci from a single slide which has been kept in storage for up to 4 years and that archival Giemsa-stained cytogenetic slide repositories represent valuable DNA resources for clinical and forensic studies.

DNA↗

DNA analysis of nosocomial infection by Enterobacter aerogenes in three cases of septicaemia in Japan.

Ceftazidime-resistant Enterobacter aerogenes was isolated from blood cultures of three patients with fever. DNA analysis using pulsed-field gel electrophoresis and ribosomal RNA gene restriction digest pattern analysis revealed that the strains were clonally similar to each other with a 79.3-96.0% homology. The same strain of E. aerogenes was isolated from a three-way stopcock connected to the indwelling catheter in one of the patients at a concentration of 45 cfu/mL. A similar strain was also isolated from the urine of one other patient on the same floor. The data suggest that E. aerogenes caused septicaemia via low bacterial contamination of a three-way stopcock in a peripheral drip intravenous infusion system in at least one patient, and that the outbreak of E. aerogenes infections was due to clonally-related strains.

Adult↗

Comparison between human and armadillo Paracoccidioides brasiliensis isolates by random amplified polymorphic DNA analysis.

Sixty-three Paracoccidioides brasiliensis isolates obtained from three nine-banded armadillos (Dasypus novemcinctus), one Amazonian armadillo's and 19 clinical isolates were compared by random amplified polymorphic DNA analysis with the primer OPG-19. The isolates were divided into three major clusters, I, II and III. Coincidences between human and armadillo isolates were observed in clusters I and II. Cluster III consisted only of armadillos' isolates. The results suggested that (I) humans may acquire P. brasiliensis infection by contact with armadillo's environment, (II) there may be P. brasiliensis genotypes peculiar to the animal, and (III) individual armadillos may be infected with P. brasiliensis cells with different genotypes.

Animals↗

MALDI-TOF mass spectrometry: a versatile tool for high-performance DNA analysis.

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has developed during the past decade into a versatile tool for biopolymer analysis. The aim of this review is to summarize this development and outline the applications, which have been enabled for routine use in the field of nucleic acid analysis. These include the analysis of mutations, the resequencing of amplicons with a known reference sequence, and the quantitative analysis of gene expression and allelic frequencies in complex DNA mixtures.

Animals↗

Plasmid DNA analysis by agarose gel electrophoresis on an epidemic-associated strain of trimethoprim resistant Shiga's bacillus from Gimira Wereda (Keffa administrative region, southwest Ethiopia).

A combination of genetic mating experiments and plasmid DNA analysis by gel electrophoresis was carried out on an epidemic-associated Shiga's bacillus with resistance type ACSSuTTp, isolated in 1983 from Gimira Wereda, Keffa Administrative Region, South West Ethiopia. The donor strain contained 9 plasmid species. Their sizes in megadaltons (Mdal) were: 120, 40, 35, 12.5, 6.0, 5.1, 4.3, 2.5 and 1.7. Analysis of Escherichia coli K12 transconjugants revealed that the 40, 35, and 4.3 Mdal plasmids coded for tetracyline-trimethoprim, ampicillin -chloramphenicol and streptomycin-sulphadiazine resistance respectively.

DNA, Bacterial↗

Image cytometric DNA analysis of adrenocortical neoplasms as a prognostic parameter: a clinico-pathologic study of 13 patients.

Formalin-fixed paraffin-embedded material of thirteen adrenocortical neoplasms were examined by conventional microscopy, and by DNA image cytometry in Feulgen-stained tissue sections and cytospin preparations. The subsequent clinical course of each patient was reviewed. Seven of the neoplasms were classified according to the histologic criteria of Weiss as adenomas and six as carcinomas. The DNA content and indices of all 13 adrenocortical neoplasms were measured by image cytometry. For the internal standard, the DNA values of the adjacent normal adrenal cells in 10 cases and of nuclei of fibrocytes of the tumour stroma were determined. DNA values in all seven adenomas, in normal adrenal cells, and in the nuclei of fibrocytes were unequivocally diploid. The six carcinomas expressed aneuploid, tetraploid or hypertetraploid DNA values. DNA values of normal adrenal cells seemed to provide a better internal control than those of connective tissue cells. Of the seven adenoma patients with a follow-up between 8 and 124 months (mean 59 months), six were alive without evidence of tumour; one patient died from other causes. Of the six carcinoma patients with a follow-up ranging from 5 days to 36 months, three patients died from the disease; one patient was alive with metastases, and only two patients were alive without evidence of the disease for 25 and 36 months, respectively. Our results strongly suggest that image cytometric DNA analysis is a valuable method to distinguish between benign and malignant adrenocortical neoplasms.

Adrenal Cortex Neoplasms↗

Differentiation of Brucella species by random amplified polymorphic DNA analysis.

Random amplification of polymorphic DNA (RAPD) was used for discrimination between 46 Brucella strains and 14 representatives of the alpha-2 and alpha-1 subgroups of Proteobacteria. To evaluate a relatively quick and exact method for Brucella identification, the authors specified the most suitable conditions for RAPD amplification of Brucella DNA with two 10-mer primers, containing lower and higher percentages of G and C. The software package PHYLIP 3.1 was used for cluster analysis of the RAPD fingerprints. The optimization of RAPD conditions resulted in PCR mixes suitable for reliable typing of Brucellae. The distance-based methods (Fitch-Margoliash, UPGMA and Neighbour-joining) gave clear discrimination between Brucella species. The constructed dendrograms put Br. canis and Br. suis bv. 1 in the same cluster and differentiated Brucella strains according to their host preferences. RAPD can be useful method to distinguish related bacterial species, and under strictly established conditions the reaction appears to be a simple, quick and sensitive technique for the epidemiological investigation of brucellosis.

Brucella↗

The four TCR genes of teleost fish: the cDNA and genomic DNA analysis of Japanese flounder (Paralichthys olivaceus) TCR alpha-, beta-, gamma-, and delta-chains.

We have isolated and identified all four TCR alpha, beta, gamma, and delta cDNAs and genomic clones from a Japanese flounder leukocyte cDNA library and bacterial artificial chromosomal genomic library. Numerous TCR transcripts were sequenced to examine the variability against antigenic peptide, and were shown hypervariability on their complementarity-determining region 3 (CDR3) loops. Among CDR3s, CDR3 delta showed a long and broad length distribution, indicating greater similarity to that of Ig. From cDNA sequences and genomic gene analysis of each chain, we found that flounder TCR beta, gamma, and delta have two different C gene segments, while the TCR alpha C region exists as a single segment. The flounder C gammas and C deltas showed different lengths in the connecting peptide (CP) region between the different types of polypeptides. The C delta 1 gene consists of two exons, one that encodes an extracellular Ig-like domain (exon 1) and the other that encodes either a very short or possibly a lacking CP region, a transmembrane region, and a cytoplasmic tail (exon 2); these are located within TCR alpha gene locus. Southern blot analysis, using the bacterial artificial chromosomal genomic DNA clones, revealed that the C delta 2 gene segment, which has a long CP region and different genomic organization to the C delta 1 gene, exists on same gene locus as the TCR gamma-chain. This suggests that the flounder possesses very unique genomic DNA organization and gene loci for TCR, C alpha/C delta 1, and C gamma/C delta 2.

Amino Acid Sequence↗

Comparison of Mycoplasma ovipneumoniae isolates using bacterial restriction endonuclease DNA analysis and SDS-PAGE.

Sixteen isolates of Mycoplasma ovipneumoniae recovered from the nasal tract or lungs of sheep from different flocks in New Zealand were examined by bacterial restriction endonuclease DNA analysis (BRENDA) using EcoR1 and by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). All isolates gave BRENDA patterns which differed entirely from one another. Following 20 serial passages (corresponding to approximately 67 generations) of an isolate, no change was detected in the BRENDA pattern. When eight isolates were examined by SDS-PAGE most bands were common but, nevertheless, each isolate was unique in the sense that they differed from one another in one or more bands. The marked heterogeneity of patterns observed when strains of M. ovipneumoniae are compared by BRENDA, together with the stability of such patterns over many generations, will enable this approach to be used to study the epidemiology of individual strains of M. ovipneumoniae within a flock.

Animals↗

DNA analysis in disputed parentage: the occurrence of two apparently false exclusions of paternity, both at short tandem repeat (STR) loci, in the one child.

In cases of disputed paternity investigated by DNA analysis, it is generally accepted that at least two independent exclusions be observed before concluding that a putative father is not the biological father of the child. We report here a case in which two apparent exclusions of paternity were obtained (at the loci FESFPS and TPOX), from a total of nineteen loci examined (short tandem repeats, AMFLPs, DQA1, Polymarkers). The combined paternity index of the other seventeen loci, and of two multilocus probes (33.15 and 33.6) would exceed twenty-eight trillion to one. In the absence of any alternative putative father (including close relatives of the man tested), we concluded that the most likely explanation for these results was that the putative father was indeed the biological father, but that two independent mutations had occurred in either the ovum and/or spermatozoon. We have altered our internal laboratory criterion for exclusion of paternity to require exclusions in three independent loci.

Alleles↗

Flow cytometric DNA analysis: a prognostic tool in non-Hodgkin's lymphoma.

Surgical biopsies from 234 untreated patients with non-Hodgkin's lymphoma (NHL), classified according to the Kiel nomenclature, were analysed with respect to proliferative activity (S-phase) and DNA content by flow cytofluorometric (FCF-DNA) analysis. The percentage of cells in S-phase was significantly higher in lymphomas of high compared to low grade NHL (p less than 0.001). Patients with lymphomas of high grade histology and low S-phase values (less than 5.6%) achieved complete remission (CR) more often (p less than 0.05) and survived significantly longer than those with high S-phase values (p less than 0.05). In the low grade NHL group the S-phase value did not correlate to response. S-phase correlated to survival for patients with the lymphocytic (CLL & IC) (p less than 0.05) and follicle center cell (FCC) derived (p less than 0.01) but not in blastic (LB, IB, Burkitt) NHL. DNA-aneuploidy was associated with poor response to therapy and shorter CR duration in low grade NHL (p less than 0.05 for both). However, the degree of DNA-ploidy (neardiploid or aneuploid) did not correlate to survival in any of the NHL groups analysed (high- or low grade, lymphocytic, FCC derived or blastic). The Cox regression analysis indicated that the S-phase value was a stronger predictor of survival than histopathology, stage or age, especially in low grade NHL. These results suggest that S-phase analysis should be included in the clinical evaluation of NHL patients as a prognostic indicator.

DNA↗

Long QT syndrome in children: the value of rate corrected QT interval and DNA analysis as screening tests in the general population.

OBJECTIVE: To evaluate two hypothetical screening strategies for identifying children with long QT syndrome (LQTS), a cause of sudden death in childhood. METHODS: Families with KVLQT1, HERG, or SCN5A genotypes provided electrocardiographic (ECG) data for this analysis. This is the first time such genotype-phenotype information has been available. Using the LQTS genotype, the distributions of QTc in affected and unaffected children were established and screening performance for various QTc cut off points were modelled. The detection rate for DNA mutation analysis was determined from published experience. RESULTS: The mean QTc (SD) was 0.484 seconds (0.031) in 117 affected children and 0.420 seconds (0.021) in 133 unaffected children. A QTc cut off of 0.50 seconds in a population of 1 million children would identify 61 of the 200 affected children, and 100 unaffected children. Estimates of testing costs for a screening programme in the newborn period would be $327 869/case detected and $2 222 000/death avoided. Although not presently available for routine use, DNA analysis could, theoretically, identify 100 of the 200 children with LQTS within the same population, along with an estimated 100 unaffected children. CONCLUSION: The only available screening test for LQTS is ECG measurement. If DNA technology becomes available for screening, unit costs must be very low to be competitive. There are multiple problems with screening for LQTS: only a minority of children will be detected, cost/death avoided is high, and pilot studies would need to be in place for 5-10 years to document efficacy.

Adolescent↗

Improved preparation technique of cervical carcinoma for flow cytometric DNA analysis with tissue disintegration in hydrochloric acid.

An one-step procedure using a nuclear isolation medium containing propidium iodide has been found to be a suitable preparation technique for flow cytometric DNA analysis in breast cancer samples. In the case of cervical squamous carcinoma, a pretreatment with HCl seems to be a methodological improvement. One advantage with the HCl modification is that some "false" near-diploid cell populations are abolished. These "false" G0/G1 peaks may represent diploid nuclei with a different stainability for propidium iodide compared to normal diploid nuclei. The HCl treatment has, furthermore, the advantage of increasing the elution of nuclei (mean factor of 4.0), especially non-diploid nuclei from higher differentiated squamous carcinomas.

Cell Nucleus↗

Identification and DNA fingerprinting of Legionella strains by randomly amplified polymorphic DNA analysis.

The randomly amplified polymorphic DNA (RAPD) technique was used in the development of a fingerprinting (typing) and identification protocol for Legionella strains. Twenty decamer random oligonucleotide primers were screened for their discriminatory abilities. Two candidate primers were selected. By using a combination of these primers, RAPD analysis allowed for the differentiation between all different species, between the serogroups, and further differentiation between subtypes of the same serogroup. The usefulness of RAPD analysis was also evaluated with outbreak-related clinical and environmental isolates previously typed by the restriction fragment length polymorphism technique. RAPD analysis proved to be as accurate as other genotypic methods, reproducible, and highly discriminatory and is a valuable new alternative to traditional fingerprinting and identification of Legionella species and strains.

Animals↗