Plasminogen activator inhibitor-1 C/G polymorphism in relation to plasma levels in rheumatoid arthritis.

Plasminogen activator inhibitor type 1 (PAI-1) is an inhibitor of plasmin production. Plasmin can directly or indirectly to degrade cartilage and bone matrix. The PAI-1 HindIII polymorphism has been associated with high PAI-1 plasma levels in myocardial infarction patients and control populations. Furthermore, it has been associated with the angiographic extent of coronary artery disease, but their involvement in other diseases is still uncertain. Here, we assessed the relationship between PAI-1 HindIII polymorphism and PAI-1 plasma levels in rheumatoid arthritis (RA). One hundred and twenty-five RA patients and 132 control subjects (CS) were included. Genotypes were identified by the polymerase chain reaction-restriction fragment length polymorphism technique and PAI-1 plasma levels were quantified using an ELISA kit. Not significant differences in genotype and allele frequencies between both studied groups were observed (P > 0.05). RA patients showed lower PAI-1 plasma levels (18.92 +/- 12.94 ng/ml) than CS (23.68 +/- 23.38 ng/ml), without significant difference (P = 0.299). However, in RA patients the C/G genotype carriers showed higher PAI-1 plasma levels (23.00 +/- 13.81 ng/ml) with respect to C/C (16.77 +/- 11.97 ng/ml) and G/G (10.47 +/- 7.07 ng/ml) genotype carriers (P = 0.036). The PAI-1 HindIII polymorphism was not associated with RA susceptibility. However, the C/G genotype is associated with high PAI-1 plasma levels in RA patients.

Equal proportions of affected cells in muscle and blood of a mosaic carrier of facioscapulohumeral muscular dystrophy.

Autosomal dominant facioscapulohumeral muscular dystrophy (FSHD) is associated with contractions of D4Z4 repeat on 4q35. It displays a remarkable inter- and intra-familial clinical variability ranging from severe phenotype to asymptomatic carriers. Mosaicism for the contracted FSHD-sized allele is a recurrent finding, but only DNA from lymphocytes had been studied. It is currently not known if mosaicism is unequally distributed between different tissues and if muscle is relatively spared for the presence of the disease allele in mosaic asymptomatic carriers of a disease allele. Here we compare DNA extracted from peripheral blood lymphocytes (PBL), fibroblasts and muscle from a mosaic asymptomatic female carrier and mother of a FSHD patient. PFGE analysis showed a complex allelic segregation: two independent mitotic rearrangement episodes occurred, resulting in mosaicism for a contracted D4Z4 repeat on 4q35 in the mother and mosaicism for an expanded D4Z4 repeat on 10q26 in the affected daughter. The results show that the proportion of mosaicism in PBL and muscle were comparable, while in fibroblasts there was some variation in the mosaicism, which might be caused by culturing artefacts. This finding supports the hypothesis that a mitotic contraction of D4Z4 is an early embryonic event and indicates that the degree of mosaicism in PBL is representative for that of muscle.

Use of single-enzyme amplified fragment length polymorphism for typing Pasteurella multocida subsp. multocida isolates from pigs.

Single-enzyme amplified fragment length polymorphism (SE-AFLP) analyses were used to differentiate 97 isolates of porcine Pasteurella multocida subsp. multocida. The strains, isolated from animals with pneumonia, rhinitis, and septicemia, were classified as capsular types A, D, and F. SE-AFLP showed a discriminatory index of 0.87 and identified 18 different profiles.

A procedure of silver staining for nucleic acids in agarose gels without pretreatment or drying steps.

In this paper, we report a fast, simple, and reproducible staining protocol for nucleic acids in agarose gels with a sensitivity in the order of 10 pg/mm2. It took only three steps: fixation, incubation with silver ions, and development of the gels (total time 50 min). The resulting calibration curves (area vs ng of loaded DNA) after a densitometric scanning of agarose gels stained with this procedure were linear up to 50 ng of double-stranded DNA. We found this method suitable for routine laboratory use and especially appropriate for densitometric analysis due to homogeneous background development. Furthermore, it avoids the pretreatment and/or drying steps proposed by other authors for agarose gels.

Repetitive DNA sequences as an insight into Aeglidae (Crustacea, Anomura) evolution.

The evolutionary relationships of five Atlantic Aeglidae species (Aegla neuquensis affinis, A. humahuaca, A. jujuyana, A. platensis, and A. uruguayana) were studied by (i) satellite DNA analysis using a restriction enzyme digestion and hybridization pattern approach and (ii) genome screening by using randomly amplified polymorphic DNA (RAPD) typing. The identical restriction patterns and intense interspecific hybridization patterns obtained in this study strongly suggest a recent cladogenetic event for the Aeglidae. The species-specific amplification products which were detected using RAPD markers allowed species characterization. A total of 49 amplification products were used to construct trees by cluster analysis. The new scheme agrees in part with previous proposals based on biogeography and morphology. We considered that the subdivision northwestern-platensis species was probably due to the rising of the Andes, which started in the Middle Miocene. Divergence due to altitude is suggested by the different altitudinal distribution of three northwestern species along the same river. The possible role of selection by ecological factor/s was observed at the population level in A. jujuyana, which has a wider altitudinal range distribution. RAPD markers revealed a high level of intraspecific diversity and important genetic flow among populations. However, a few markers showed significant differences in frequency or H between the lowermost population and the other populations, located in a different biogeographical region. The differences were not in relation to geographical distance, and we interpreted them as being due to selection. Repetitive sequences constitute an important reservoir of genetic variation, and these results show their usefulness in testing and proposing evolutionary hypothesis in crabs. These sequences seem to have played an important role in aeglid evolution. Ecological factors related to altitude have probably influenced macro- and microevolutionary processes, at least in northwestern species.

In-frame cloning of large synthetic genes using moderate-size oligonucleotides.

A method is described that facilitates the cloning of large synthetic genes in plasmid vectors such as pUC and pGEM. This protocol uses unpurified synthetic oligonucleotides of moderate length (ca. 50-90 bp) to construct larger DNA molecules by a reiterative, directional cloning procedure. Open reading frames are maintained by the flexible use of six-base pair blunt-end restriction sites that are not present in the DNA sequence of the plasmid cloning vector. Rapid production and analysis of plasmid intermediates are achieved by standard recombinant DNA cloning methods. The use of an anchored sticky-end restriction site and a variable blunt-end restriction site in each step of the cloning scheme gives specific orientation to each oligonucleotide fragment and results in high cloning efficiencies. The flexibility of the method allows for the construction of a gene of any size. Very large synthetic genes can be made by generating the intermediate gene fragments in parallel vectors and simply cloning the fragments in frame to produce the final construct.

Restriction endonuclease analysis of Staphylococcus aureus plasmid DNA from three continents.

Staphylococcus aureus isolates (n = 1201) from 20 centers in Europe, the USA and Brazil were evaluated for the presence of epidemiologic markers. Plasmid typing and restriction endonuclease analysis of plasmid DNA confirmed the presence of an apparently identical plasmid in 13% of clinical isolates. The plasmid was recovered from all 20 hospitals studied, with an overall frequency of greater than 10% on each of the three continents. Since relatively few staphylococcal plasmids may be shared by epidemiologically unrelated strains, there are inherent limitations to this otherwise useful technique. Additionally, these data demonstrate the importance of including unrelated strains of Staphylococcus aureus from the local region as controls when molecular typing methods are performed.

Use of DNA restriction endonuclease digest and ribosomal RNA gene probe patterns to fingerprint Helicobacter pylori and Helicobacter mustelae isolated from human and animal hosts.

Variation amongst strains of Helicobacter pylori and Helicobacter mustelae was examined by DNA restriction endonuclease digestion and rRNA gene patterns generated using a non-radioactive probe. Chromosomal DNA was extracted from 30 cultures of H. pylori from human, Rhesus monkey and pig gastric mucosa, and from three H. mustelae isolates from ferret gastric mucosa. DNA fingerprinting with Hae III and Hind III showed H. mustelae was relatively homogeneous but revealed genomic heterogeneity within H. pylori with at least 18 different DNA patterns identifiable amongst the 30 isolates. Five sets of strains other than duplicates with matching DNA fingerprints were identified within H. pylori. The Peruvian isolates were the largest identical set and comprised eight isolates from four different patients with five consecutive isolates from one patient. The Rhesus monkey strains were a relatively homogeneous set as were several Australian human isolates. The study demonstrates that rRNA gene restriction patterns provide a simple but highly discriminatory electrophoretic fingerprint for H. pylori with potential for use as a novel epidemiological marker in addition to total DNA digest analysis.