Molecular diagnostics on microfabricated electrophoretic devices: from slab gel- to capillary- to microchip-based assays for T- and B-cell lymphoproliferative disorders. (65/3912)

BACKGROUND: Current methods for molecular-based diagnosis of disease rely heavily on modern molecular biology techniques for interrogating the genome for aberrant DNA sequences. These techniques typically include amplification of the target DNA sequences followed by separation of the amplified fragments by slab gel electrophoresis. As a result of the labor-intensive, time-consuming nature of slab gel electrophoresis, alternative electrophoretic formats have been developed in the form of capillary electrophoresis and, more recently, multichannel microchip electrophoresis. METHODS: Capillary electrophoresis was explored as an alternative to slab gel electrophoresis for the analysis of PCR-amplified products indicative of T- and B-cell malignancies as a means of defining the elements for silica microchip-based diagnosis. Capillary-based separations were replicated on electrophoretic microchips. RESULTS: The microchip-based electrophoretic separation effectively resolved PCR-amplified fragments from the variable region of the T-cell receptor-gamma gene (150-250 bp range) and the immunoglobulin heavy chain gene (80-140 bp range), yielding diagnostically relevant information regarding the presence of clonal DNA populations. Although hydroxyethylcellulose provided adequate separation power, the need for a coated microchannel for effective resolution necessitated additional preparative steps. In addition, preliminary data are shown indicating that polyvinylpyrrolidone may provide an adequate matrix without the need for microchannel coating. CONCLUSIONS: Separation of B- and T-cell gene rearrangement PCR products on microchips provides diagnostic information in dramatically reduced time (160 s vs 2.5 h) with no loss of diagnostic capacity when compared with current methodologies. As illustrated, this technology and methodology holds great potential for extrapolation to the abundance of similar molecular biology-based techniques.  (+info)

Plastic microchip electrophoresis for analysis of PCR products of hepatitis C virus. (66/3912)

BACKGROUND: Electrophoresis on polymeric rather than glass microstructures is a promising separation method for analytical chemistry. Assays on such devices need to be explored to allow assessment of their utility for the clinical laboratory. METHODS: We compared capillary and plastic microchip electrophoresis for clinical post-PCR analysis of hepatitis C virus (HCV). For capillary electrophoresis (CE), we used a separation medium composed of 10 g/L hydroxypropyl methyl cellulose in Tris-borate-EDTA buffer and 10 micromol/L intercalating dye. For microchip electrophoresis, the HCV assay established on the fused silica tubing was transferred to the untreated polymethylmethacrylate microchip with minimum modifications. RESULTS: CE resolved the 145-bp amplicon of HCV in 15 min. The confidence interval of the migration time was <3.2%. The same HCV amplicon was resolved by microchip electrophoresis in <1.5 min with the confidence interval of the migration time <1.3%. CONCLUSION: The polymer microchip, with advantages that include fast processing time, simple operation, and disposable use, holds great potential for clinical analysis.  (+info)

Ratio of remnant-like particle-cholesterol to serum total triglycerides is an effective alternative to ultracentrifugal and electrophoretic methods in the diagnosis of familial type III hyperlipoproteinemia. (67/3912)

BACKGROUND: Familial type III hyperlipoproteinemia (HLP) is characterized by the presence of beta-migrating VLDL (beta-VLDL) and increased risk of cardiovascular disease. Assessment of plasma beta-VLDL is achieved by measuring the ratio of VLDL-cholesterol (VLDL-C) to total plasma triglycerides (TGs) or by detecting beta-VLDL in total VLDL. The objective of this study was to compare the clinical utility of the ratio of remnant-like particle-cholesterol (RLP-C) to total TGs with that of the current methods for diagnosing type III HLP. METHODS: Detection of beta-VLDL by electrophoresis of VLDL was used to define type III HLP. Twenty-eight patients with type III HLP and 43 subjects lacking beta-VLDL were investigated. Fasting TG concentrations were >2.26 mmol/L in all subjects. Subjects were separated into three groups: group 1, serum total cholesterol 5.18 mmol/L and TGs between 2.26 and 9.04 mmol/L (n = 51); and group 3, TGs >9.04 mmol/L (n = 9). RESULTS: In group 2, a RLP-C-to-total TG molar ratio >/=0.23 (>/=0.10 when using mg/dL) and a VLDL-C-to-total TG molar ratio >/=0.69 (>/=0.30 when using mg/dL) correctly classified 94% and 90% of the subjects, respectively. The utility of the RLP-C-to-total TG ratio in diagnosing type III HLP decreased in patients in the other two groups. CONCLUSION: When used in an appropriate target population, the RLP-C-to-total TG ratio is a convenient and effective alternative to ultracentrifugal and electrophoretic methods for diagnosing type III HLP.  (+info)

Current techniques in protein glycosylation analysis. A guide to their application. (68/3912)

The importance of glycosylation in biological events and the role it plays in glycoprotein function and structure is an area in which there is growing interest. In order to understand how glycosylation affects the shape or function of a protein it is however important to have suitable techniques available to obtain structural information on the oligosaccharides attached to the protein. For many years the complexity of the structures required sophisticated analytical techniques only available to a few specialist laboratories. In many cases these techniques were not available or required a large amount of material and therefore the number of glycoproteins which were fully characterised were relatively few. In recent years there have been substantial developments in the analysis of glycosylation which has significantly changed the capability to fully characterise molecules of biological interest. A number of different techniques are available which differ in terms of their complexity, the amount of information which is available from them, the skill needed to perform them and their cost. It is now possible for many laboratories who do not specialise in glycosylation analysis to obtain some information although this may be incomplete. These developments do, however, also make complete characterisation of a glycoprotein a much less daunting task and in many cases this can be performed more easily and with less starting material than was previously required. In this review a summary will be given of current techniques and their suitability for different types of analysis will be considered.  (+info)

Counter-electrophoresis as a possible method for typing ECHO and Coxsackie B viruses. (69/3912)

A method for typing ECHO and Coxsackie B viruses using counter-electrophoresis has been developed using stock strains of 15 different ECHO types and 5 Coxsackie B viruses. Work is continuing to see whether the method is a practical one to use for typing of strains from patients infected with ECHO or Coxsackie B viruses.  (+info)

Genetically distinct dog-derived and human-derived Sarcoptes scabiei in scabies-endemic communities in northern Australia. (70/3912)

Overcrowding is a significant factor contributing to endemic infection with Sarcoptes scabiei in human and animal populations. However, since scabies mites from different host species are indistinguishable morphologically, it is unclear whether people can be infected from scabies-infested animals. Molecular fingerprinting was done using three S. scabiei-specific single locus hypervariable microsatellite markers, with a combined total of 70 known alleles. Multilocus analysis of 712 scabies mites from human and dog hosts in Ohio, Panama and Aboriginal communities in northern Australia now shows that genotypes of dog-derived and human-derived scabies cluster by host species rather than by geographic location. Because of the apparent genetic separation between human scabies and dog scabies, control programs for human scabies in endemic areas do not require resources directed against zoonotic infection from dogs.  (+info)

Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya. (71/3912)

SDS-PAGE of total bacterial proteins was applied to the classification of 25 Sudanese and five Kenyan strains isolated from the root nodules of Acacia senegal and Prosopis chilensis. Twenty strains were also studied by multilocus enzyme electrophoresis (MLEE) and the whole 16S rRNA gene was sequenced from two strains representing the two major clusters. These results, together with the previously reported numerical taxonomy analysis, pulsed-field gel electrophoresis studies, DNA-DNA dot-blot hybridization, genomic fingerprinting using repetitive sequence-based PCR, DNA base composition analysis, DNA-DNA reassociation analysis, partial sequencing of the 16S rRNA gene and RFLP analysis of the amplified 16S rRNA gene, showed that all 30 strains belong to the genus Sinorhizobium. Two of the strains grouped with Sinorhizobium saheli and seven with Sinorhizobium terangae, while the rest did not cluster with any of the established species. The majority of the strains formed two phenotypically and genotypically distinct groups and we therefore propose that these strains should be classified as two new species, Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov.  (+info)

Rhizobium etli bv. mimosae, a novel biovar isolated from Mimosa affinis. (72/3912)

Fifty rhizobial isolates from root nodules of Mimosa affinis, a small leguminous plant native to Mexico, were identified as Rhizobium etli on the basis of the results of PCR-RFLP and RFLP analyses of small-subunit rRNA genes, multilocus enzyme electrophoresis and DNA-DNA homology. They are, however, a restricted group of lineages with low genetic diversity within the species. The isolates from M. affinis differed-from the R. etli strains that orginated from bean plants (Phaseolus vulgaris) in the size and replicator region of the symbiotic plasmid and in symbiotic-plasmid-borne traits such as nifH gene sequence and organization, melanin production and host specificity. A new biovar, bv. mimosae, is proposed within R. etli to encompass Rhizobium isolates obtained from M. affinis. The strains from common bean plants have been designated previously as R. etli bv. phaseoli. Strains of both R. etli biovars could nodulate P. vulgaris, but only those of bv. mimosae could form nitrogen-fixing nodules on Leucaena leucocephala.  (+info)