Methods for pulsed-field gel electrophoresis

Pulsed Field Gel Electrophoresis: Past, present, and future

Pulsed Field Gel Electrophoresis (PFGE) has been considered for many years the 'gold-standard' for characterizing many pathogenic organisms as well as for subtyping bacterial species causing infection outbreaks. This article reviews the basic principles of PFGE and it includes the main advantages and limitations of the different electrode configurations that have been used in PFGE equipment and their influence on the DNA electrophoretic separation. Remarkably, we summarize here the most relevant theoretical and practical aspects that we have learned for more than 20 years developing and using the miniaturized PFGE systems. We also discussed the theoretical aspects related to DNA migration in PFGE agarose gels. It served as the basis for simulating the DNA electrophoretic patterns in CHEF mini gels and mini-chambers during experimental design and optimization. A critical comparison between standard and miniaturized PFGE systems, as well as the enzymatic and non-enzymatic methods for intact immobilized DNA preparation, is provided throughout the review. The PFGE current applications, advantages, limitations and future challenges of the methodology are also discussed.

Analyzing Copy Number Variation Using Pulsed-Field Gel Electrophoresis: Providing a Genetic Diagnosis for FSHD1

The myopathy facioscapulohumeral muscular dystrophy type 1 (FSHD1) is caused by copy number variation of the D4Z4 macrosatellite repeat on chromosome 4. In unaffected individuals the number of 3.3 kb D4Z4 units varies between 8 and 100, whereas 1-10 units are seen in FSHD1 cases. A homologous and heterogenous D4Z4 array can be found on chromosome 10q, but contractions of this array are typically not associated with FSHD. Discriminating between the chromosome 4 and chromosome 10 D4Z4 arrays, as well as determining the array size, requires the use of pulsed-field gel electrophoresis, Southern blotting, and the isolation of high-quality DNA.

Somatic mosaicism in FSHD often goes undetected

Autosomal dominant facioscapulohumeral muscular dystrophy (FSHD1A) is associated with contractions of the polymorphic D4Z4 repeat array on chromosome 4qter. The disease has a high frequency of new mutations of mitotic origin. Pulsed-field gel electrophoresis-based studies show that mitotic mutations leading to somatic mosaicism occur equally frequently in patients and parents. Nevertheless, somatic mosaicism in FSHD is mainly reported in asymptomatic parents by applying standard Southern analysis after linear gel electrophoresis. Explaining this apparent discrepancy, we here demonstrate that somatic mosaicism in FSHD patients goes largely undetected using the standard diagnostic technique, indicating that linear electrophoresis is unsuitable to identify mosaic patients. As a consequence, the phenotype of mosaic patient's offspring will be underestimated, whereas the recurrence risk in the symptomatic mosaic individuals will be overestimated. Moreover, somatic mosaicism may partly explain the observation of anticipation in de novo kindreds. Therefore, clinicians should always consider pulsed-field gel electrophoresis analysis in de novo FSHD families, in particular when the patient's phenotype is much milder than expected based on D4Z4 length proper.

Phenotypic variability of Filipino beta(o)-thalassemia/HbE patients in Indonesia

Three Indonesian patients with identical genotypes, each compound heterozygotes for Filipino beta(o)-thalassemia/HbE, expressed different clinical severities. One patient has mild disease and is transfusion independent, while the other two are severely affected and transfusion dependent. The size of the Filipino beta(o)-globin gene deletion was confirmed to be 45 kb, resolving conflicting values given in the literature. Neither ameliorating genetic factors such as alpha-globin gene deletions or the XmnI restriction site polymorphism at position -158 upstream of the (G)gamma-globin gene, nor differences in beta-globin gene haplotype, explain the phenotypic variation. These observations have implications for the development of antenatal diagnosis in Indonesia, as at present it is not possible to give an accurate prediction of severity of phenotype for this common genotype.

DNA based typing, identification and detection systems for food spoilage microorganisms: development and implementation

The rapid identification of spoilage microorganisms is of eminent importance to the food industry. It provides the food industry with the opportunity to reduce economical losses by designing adequate intervention measures. The use of identification systems based on biochemical and physiological characteristics resulted often in disappointing identification results and misidentifications. This will inevitably lead to inappropriate strategies to prevent spoilage. This review discusses the potential of the DNA based identification technology including the polymerase chain reaction (PCR) for the identification and specific detection of microorganisms. Fingerprinting methods based on the DNA-probe technology enable a clear insight in the identity of microorganisms on different levels, varying from genus to strain level depending on the systems used. Discrimination between subspecies and strain level is shown to be helpful for investigating routes and sources of contamination. Differentiation at the species level is demonstrated to be essential in order to design a highly specific detection system enabling to signalize a microorganism that belongs to a particular species. Also indicated in this review is the necessity and the technical approach to detect microorganisms that display a particular undesirable trait.

A new mobile genetic element in Lactobacillus delbrueckii subsp. bulgaricus

A new IS element (ISL3) was discovered in Lactobacillus delbrueckii subsp. bulgaricus during the characterization of the linkage relationships between the two genes important for milk fermentation, beta-galactosidase (lacZ) and the cell-wall associated protease (prtP). ISL3 is a 1494 bp element, flanked by 38 bp imperfect inverted repeats, and generates an 8 bp target duplication upon insertion. It contains one open reading frame, encoding a potential polypeptide of 434 amino acids, which shows significant homology (34% identity) to the transposase of the Leuconostoc mesenteroides element IS1165. Molecular analysis of spontaneous lacZ mutants revealed some strains that had sustained deletions of 7 to 30 kb in size, centered on and eliminating the copy of ISL3 next to lacZ. Other deletion endpoints were identified as located immediately adjacent to ISL3. Furthermore, genetic translocations that had occurred via transposition of ISL3 were observed fortuitously in cultures screened for deletion mutants. ISL3 can be found in one to several copies in various strains of L. delbrueckii. However, it was not present in other dairy lactic acid bacteria tested.