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PubMed2006

Identification of SYT-SSX transcripts from synovial sarcomas using RT-multiplex PCR and capillary electrophoresis.

Synovial sarcomas are highly malignant tumors of soft tissue which are characterized by the t(X;18) resulting in SYT-SSX fusion transcript production. Diagnosis of these tumors based on histology can be challenging, particularly when minimal biopsy specimens are presented to the pathologist. Demonstration by molecular methods of SYT-SSX transcripts is a useful adjunct for diagnosis in these situations. We have developed an assay, which combines one-step RT-multiplex PCR with capillary electrophoresis to detect and genotype the SYT-SSX transcripts from synovial sarcomas. Small amplicons from chimeric transcripts as well as GAPD transcripts are differentially labeled with fluorophores, allowing detection and size discrimination by capillary electrophoresis. In a study of 32 formalin-fixed soft tissue tumor specimens, the assay detected chimeric transcripts from 17/22 (77%) synovial sarcomas. All five assay negative specimens yielded no intact RNA as evidenced by lack of a GAPD amplicon. Chimeric transcripts were not detected in 9/9 malignant peripheral nerve sheath tumors or 1/1 epithelioid sarcoma. Representative amplicons were sequenced and confirmed the genotype results obtained by capillary electrophoresis. One-step RT-multiplex PCR combined with capillary electrophoresis is a rapid and accurate method for the detection and genotypic classification of SYT-SSX transcripts from fixed tissue specimens.

Adolescent↗

PubMed1993

Agarose gel electrophoresis system for the separation of antibiotics used in animal agriculture.

A novel electrophoresis system using agarose gel has been developed for the separation and as an aid in the classification of antibiotics. This system utilizes Nunc cell factory disposable tissue culture dishes, which serve as bioassay dish and cooling chamber for agarose gel, in a custom designed electrophoresis unit. Tris(hydroxymethyl) methylamine-succinate buffer at pH 6.0 and 8.0 are employed as the electrolyte for electrophoresis. Bioautography was used as the indicator of mobility. Any agar diffusion assay can be modified to use this system. A suggested name for this system is Nunc cell factory agarose gel electrophoresis (NUAGE). Selected antibiotics, representative of the aminoglycoside, beta-lactam, macrolide, moenocinol, peptide, polyene, polyether, quinone and tetracycline classes, were separated with this system.

Animal Feed↗

PubMed1971

Protein-bound phosphorylserine in acid hydrolysates of brain tissue. The determination of ( 32 P)phosphorylserine by ion-exchange chromatography and electrophoresis.

1. Partial acid hydrolysates of proteins derived from cortical slices of guinea-pig brain were divided into two parts and fractionated by ion-exchange chromatography and high-voltage electrophoresis. 2. The apparent yield of protein-bound phosphorylserine by the ion-exchange method was about three times that obtained by electrophoresis. 3. The specific radioactivity of phosphorylserine isolated from (32)P-labelled slices by electrophoresis was twice that isolated by chromatography. 4. The discrepancies were found to be due to the presence of unlabelled phosphates of unknown composition in the ;phosphorylserine' fraction obtained by the ion-exchange method. 5. Electrical stimulation of slices respiring in the presence of [(32)P]phosphate increased the specific radioactivity of the total phosphate in the chromatographic ;phosphorylserine' fraction by 53+/-11%, as compared with only 19+/-5% for the phosphorylserine isolated by electrophoresis.

Animals↗

PubMed1976

The instantaneous monitoring of polyacrylamide gels during electrophoresis.

The advantages of being able to see protein zones in a gel during electrophoresis (and hence before staining) are pointed out, and a method is described which depends on local increments of refractive index in these zones. The use of local increments of refractive index in polyacrylamide gels for measuring protein concentrations in zones during electrophoresis is briefly considered; it is found that such increments are greater than would be expected from the amount of protein when sodium dodecyl sulphate is present. The enhancement depends on conditions and time of running. This makes quantitative estimates difficult, but the sensitivity of detection of protein zones by observations based on refractive-index changes is greatly increased by this property of sodium dodecyl sulphate. Methods are described for making optically uniform gels (both with uniform and with graded concentrations of polyacrylamide), necessary for observation of small changes in refractive index. A simple dark-field system of observation is described. Examples are given showing protein samples observed with the system during electrophoresis and compared with the same gel stained with Coomassie Blue after completion of the run. Under optimal conditions the optical method is comparable in sensitivity with staining. With the proteins of lower mol.wt. (approx. 15000), the optical method is not so sensitive, becoming less sensitive with longer running time. This loss of sensitivity is greatly decreased by using more concentrated polyacrylamide gels, and graded gels are therefore more suitable for optical observation than are uniform gels. The observation of protein zones during electrophoresis adds nothing to the time needed for making a stained gel and gives much information long before it can be obtained from the stained gel.

Electrophoresis, Polyacrylamide Gel↗

PubMed1999

Comparative mutation detection screening of the type VII collagen gene (COL7A1) using the protein truncation test, fluorescent chemical cleavage of mismatch, and conformation sensitive gel electrophoresis.

Mutations in the type VII collagen gene, COL7A1, give rise to the blistering skin disease, dystrophic epidermolysis bullosa. We have developed two new mutation detection strategies for the screening of COL7A1 mutations in patients with dystrophic epidermolysis bullosa and compared them with an established protocol using conformational sensitive gel electrophoresis. The first strategy consisted of an RNA based protein truncation test that amplified the entire coding region in only four overlapping nested reverse transcriptase-polymerase chain reaction assays. These fragments were transcribed and translated in vitro and analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. We have used the protein truncation test procedure to characterize 15 truncating mutations in 13 patients with severe recessive dystrophic epidermolysis bullosa yielding a detection sensitivity of 58%. The second strategy was a DNA-based fluorescent chemical cleavage of mismatch (fl-CCM) procedure that amplified the COL7A1 gene in 21 polymerase chain reaction assays. Mismatches, formed between patient and control DNA, were identified using chemical modification and cleavage of the DNA. We have compared fl-CCM with conformational sensitive gel electrophoresis by screening a total of 50 dominant and recessive dystrophic epidermolysis bullosa patients. The detection sensitivity for fl-CCM was 81% compared with 75% for conformational sensitive gel electrophoresis (p = 0.37 chi2-test). Using a combination of the three techniques we have screened 93 dystrophic epidermolysis bullosa patients yielding an overall sensitivity of 87%, detecting 79 different mutations, 57 of which have not been reported previously. Comparing all three approaches, we believe that no single method is consistently better than the others, but that the fl-CCM procedure is a sensitive, semiautomated, high throughput system that can be recommended for COL7A1 mutation detection.

Collagen↗

PubMed2004

Functional genomic study on atrial fibrillation using cDNA microarray and two-dimensional protein electrophoresis techniques and identification of the myosin regulatory light chain isoform reprogramming in atrial fibrillation.

INTRODUCTION: Functional and structural changes of atrial tissue occur during the natural course of atrial fibrillation (AF), and these changes may contribute to further AF. We investigated the changes in AF tissue using cDNA microarray and two-dimensional protein electrophoresis techniques. METHODS AND RESULTS: We established a porcine model of AF by rapid right atrial appendage pacing at a rate of 600/min. Atrial tissue was obtained after rapid atrial depolarization for 6 weeks. Microarrays containing 6,035 cDNA clones were used to evaluate the alterations of mRNA. Two-dimensional protein electrophoresis was performed to compare protein patterns. In cDNA microarray studies, we identified 387 genes with significant change in the left atrium and 81 genes in the right atrium. Among the genes, the ventricular isoform of the myosin regulatory light chain (MLC-2V) showed the greatest fold of change (9.4 and 7.3 in the left and right atrium, respectively). In protein electrophoresis, the expression levels of three protein spots spanning from 18 to 20 kDa in the acidic region (PI 4.5-5.0) were specifically elevated in the AF group. Interestingly, through tandem mass spectrometric analysis, these three spots were identified as MLC-2V. Thus, MLC-2V expression at the mRNA and protein levels corresponded well, and both indicated a significant increase in AF. CONCLUSION: Both cDNA microarray and two-dimensional polyacrylamide protein electrophoresis studies revealed characteristic changes in AF tissue. We demonstrated the reprogramming of myosin regulatory light chain isoform composition, with a significant increase of its ventricular isoform (MLC-2V).

Animals↗

PubMed1997

Capillary electrophoresis of r-hirudin and a polyethylene glycol derivative of r-hirudin (PEG-hirudin).

UNLABELLED: Recombinant (r-) hirudins and PEG-hirudin are currently tested for anticoagulant therapy. For their concentration measurement, radioimmunoassay and HPLC methods are available. The separation of r- and PEG-hirudin is currently performed by HPLC. However, the sensitivity of the method is low. Capillary electrophoresis is a rapid, selective technique that requires low sample amounts. Our aim was the development of a capillary electrophoresis method to measure r- and PEG-hirudin. The results are as follows: In a borate solution (0.3% boric acid and 0.4% sodium tetraborate, pH 9.5) r-hirudin was separated from PEG-hirudin in a purified system using a fused silica capillary (50 cm long and 75-micron i.d. and reversed polarity). A neutral capillary with a 20 mM tricine buffer (pH 8.0, field strength 500 V/cm) was also effective in resolving r- from PEG-hirudin. A linear correlation was found between the peak area and the concentration between 20 micrograms/mL and 10 mg/mL for hirudin (r2 = 0.99) and between 1.25 and 10 mg/mL for PEG-hirudin (r2 = 0.99). In human plasma mixtures, r- and PEG-hirudin were completely separated. The linear correlation between the peak area and the concentration was r2 = 0.99. CONCLUSION: In a fused silica capillary, r- and PEG-hirudin are separated in a purified system. Capillary electrophoresis which is performed in a neutral capillary, resolves r- from PEG-hirudin in a purified system, in plasma and in urine. The sensitivities of the methods are comparable. Capillary electrophoresis separates r- from PEG-hirudin and may be applied to biologic systems to measure the concentration and purity of r- and PEG-hirudin.

Electrophoresis, Capillary↗

PubMed1986

[Value of lipoprotein electrophoresis for the quantitative assessment of plasma lipoproteins].

The reliability of semiquantitative densitometric lipoprotein electrophoresis was compared with that of the quantitative determination of plasma lipoproteins by zonal ultracentrifugation on plasma from 73 patients. As an alternative to the measurement of lipoproteins by electrophoresis other, simple laboratory methods were used and also compared with plasma lipoprotein concentrations obtained by zonal ultracentrifugation. It was found that quantitative measurement of plasma lipoproteins by densitometric electrophoresis correlated positively to actual plasma concentration by zonal ultracentrifugation, but other simple methods of lipid determination--of plasma cholesterol; of triglycerides; of HDL and LDL cholesterol--are definitely better for obtaining plasma lipoprotein concentrations. Lipoprotein electrophoresis should not be used for the quantitative determination of plasma lipoproteins.

Blood Protein Electrophoresis↗

PubMed1983

Novel application of H tube electrophoresis to separation technology.

The H tube electrophoresis technique was used for isolating human IgG by the net effect of electrophoresis and electro-endosmosis in agarose gel containing human serum. In a similar experiment human serum albumin was purified by extracting the agarose gel slice containing the albumin following zone electrophoresis of serum in agarose. By taking advantage of the relatively high reverse electro-endosmotic flow compared to the migration of IgG in agarose gel, sheep anti chicken immunoglobulin was fractionated into active and inactive portions. It was estimated that 90% of the nonspecific IgG could be eliminated in this manner. The specific immunoglobulin fraction showed a higher mobility to the positive electrode than the bulk of the non specific IgG. The H tube proved to be ideal for zone electrophoresis in concentration gradients of inert substances. For this purpose sugar gradients were used for electrophoretic separation of proteins and viruses which are not affected by high osmotic pressures but, for separating animal cells it was necessary to use Ficoll gradients. A mixture of yellow Atypical Tomato Mosaic Virus and the haemocyanin of Burnupena cincta were separated into discrete zones and chicken IgY anti haemocyanin was subfractionated. The specific fraction showed a lower migration rate to the positive pole than the bulk of the non specific material.

Animals↗

PubMed1990

Enzymatic and radioimmunoassay procedures combined with electrophoresis and HPLC for the recovery and characterization of substance P in human brain.

Immunoreactive substance P was recovered from human brain (hypothalamus and substantia nigra) by acetic acid extraction, ion exchange chromatography (SP-Sephadex), molecular sieving (Sephadex G-50) and column electrophoresis in agarose suspension. The chemical nature of the active material was further studied with various biochemical techniques including agarose suspension electrophoresis, HPLC and different kinds of enzyme radioimmunoassays. By combining these techniques it was possible to confirm structure identity between the recovered active component and substance P previously isolated from bovine brain. Thus, the major activity reacting with the substance P antibodies was indistinguishable from the synthetic bovine analogue in all chromatographic systems including analytical electrophoresis at different pH:s and HPLC. Furthermore, digestion of the active material with post-proline cleaving enzyme and trypsin yielded fragments identical with those expected from the bovine peptide as confirmed by specific radioimmunoassays in conjunction with electrophoresis or HPLC. The result also indicates the usefulness of the present procedures for identifying peptides structures available only in minute amounts.

Chromatography, High Pressure Liquid↗

PubMed1990

DNA double-strand break analysis by CHEF (clamped homogeneous electrical field) electrophoresis.

Pulsed-field gel electrophoresis (PFGE) has become a powerful tool for the study of high-molecular-weight DNA. In this technical note the application of clamped homogeneous electrical field (CHEF) electrophoresis for the determination of DNA double-strand breaks is described, and a number of parameters that influence the sensitivity of the assay are discussed. They include the concentration of the cell sample, agarose concentration in the plug and the electrophoresis gel, lysis conditions, pulse time, electric field gradient and the temperature of electrophoresis.

Animals↗

PubMed1994

Modifications of alkaline microgel electrophoresis for sensitive detection of DNA damage.

The alkaline microgel electrophoresis technique was modified to achieve a substantial increase in sensitivity for the detection of radiation-induced DNA damage in human lymphocytes. This increased sensitivity was achieved through: (1) the addition of free radical scavengers to the electrophoresis solution to reduce DNA damage generated during alkaline unwinding and electrophoresis; (2) the modification of the electrophoresis unit to achieve a more uniform electric field; (3) the use of YOYO-1, a DNA dye, producing fluorescence 500-fold more intense than ethidium bromide; and (4) the introduction of an image analysis system for the quantitation of DNA migration. In addition to increasing sensitivity, these modifications have increased the speed with which observations can be quantified, and improved reproducibility from experiment to experiment. In human lymphocytes, these modifications have resulted in an increased sensitivity of several fold, allowing the detection of DNA damage in the range of 50 mGy. This increased sensitivity for the detection of DNA damage should extend the utility of this technique.

Benzoxazoles↗

PubMed1991

Application of multilocus enzyme electrophoresis to epidemiologic investigations of Xanthomonas maltophilia.

OBJECTIVE: To test the utility of a newly developed multilocus enzyme electrophoresis typing method for Xanthomonas maltophilia. DESIGN: Isolates were first screened by slide agglutination, which served as the standard to characterize the outbreak strains. All isolates were then subjected to multilocus enzyme electrophoresis and the results analyzed based on epidemiological data. SETTING: This outbreak occurred in a shock-trauma intensive care unit of a large general community hospital. PATIENTS: Patients admitted to the shock-trauma intensive care unit who had X maltophilia isolated from any site greater than or equal to 24 hours after admission met the case definition. Specimens from patients who fit the case definition were characterized, as were specimens from other patients that were used as controls for nonoutbreak isolates. Environmental samples were also evaluated for X maltophilia. RESULTS: Most of the 64 isolates received during this outbreak were serotype 10, and when they were subjected to multilocus enzyme electrophoresis, one electrophoretic type predominated and correlated to most outbreak isolates. Unrelated isolates of serotype 10 from other institutions all exhibited unique electrophoretic types. CONCLUSION: Application of multilocus enzyme electrophoresis to X maltophilia outbreaks is a valuable addition to the characterization of suspected outbreak strains.

Bacterial Infections↗

PubMed1996

Mutational scanning of large genes by extensive PCR multiplexing and two-dimensional electrophoresis: application to the RB1 gene.

With the rapid increase in the number of identified human disease genes, the development of accurate and cost-efficient mutation tests has become opportune. Here we present a combination of extensive PCR multiplexing and two-dimensional (2-D) DNA electrophoresis to screen for mutations in 26 exons of the retinoblastoma (RB1) tumor suppressor gene. In 2-D electrophoresis, fragments are separated according to size and base pair sequence in non-denaturing and denaturing gradient gels, respectively. All target fragments, designed to have optimal melting characteristics, were prepared in a two-step PCR (a 6-plex long-PCR pre-amplification and a subsequent 25-plex short-PCR) followed by heteroduplexing. The mixture of PCR amplicons was then subjected to 2-D electrophoresis under a single set of experimental conditions. With this design, 35 previously identified mutations in 18 different exons were detected in 33 bilateral retinoblastoma patients. These results suggest that 2-D electrophoresis in this format provides a generally applicable, practical and fast way to diagnose with high accuracy large genes for a broad spectrum of possible disease-causing mutations.

DNA Mutational Analysis↗

PubMed1998

Single cell gel electrophoresis assay: sensitivity of peripheral white blood cells in human population studies.

The single cell gel electrophoresis assay (Comet assay) was selected as a biomarker of exposure to evaluate the impact of air pollution and lifestyle variables on hospitalized pregnancies in two districts with different air pollution levels in northern (Teplice) and southern (Prachatice) Bohemia. The hypothesis was that the DNA damage detected as single strand breaks would be generally higher in the district with higher air pollution levels. To undertake the study we enrolled 322 pregnancies in Teplice and 220 in Prachatice. Venous and cord blood were analysed using the original alkaline Comet assay procedure with lysis for 60 min, unwinding for 40 min and electrophoresis for 24 min. We also used a modified procedure in which unwinding was prolonged to 60 min and electrophoresis to 40 min. Peripheral white blood cells (WBC) were analysed using an image analyser system. When we analysed the results obtained for mothers and their children no differences were found between polluted and control districts. The prolongation of alkali unwinding and electrophoresis did not increase sensitivity of the assay. No effects of prematurity, ethnicity, smoking or GSTM1 polymorphism were observed for any of the Comet parameters. Multiple regression analyses were performed for the European population (n = 285). A statistical model was fitted to determine the relationship between the Comet parameters of mothers and their children. According to our results it seems that the Comet assay was not a particularly sensitive technique to determine the effects of environmental pollution at the DNA level if peripheral WBC are used.

Air Pollutants↗

PubMed1989

Determination of microbial genome sizes by two-dimensional denaturing gradient gel electrophoresis.

In two-dimensional denaturing gradient gel electrophoresis, DNA is digested with a restriction endonuclease and the resulting DNA fragments are separated as a function of size by conventional agarose gel electrophoresis. Following this first dimension electrophoresis, the fragment distribution is placed at the top of a denaturing gradient slab gel and electrophoresis is carried out parallel to the gradient direction. This second dimension separation is a complex function of the base sequence of each fragment. Analysis of the DNA fragment distribution as a function of fragment size allows the DNA size to be calculated. This method has been applied to calculate three microbial genome sizes: Mycoplasma capricolum, 724 kb; Acholeplasma laidlawii, 1646 kb; and Hemophilus influenzae, 1833 kb.

Acholeplasma↗

PubMed1978

Separation of very large DNA molecules by gel electrophoresis.

Very large DNA molecules were separated by electrophoresis in horizontal slab gels of dilute agarose. Conditions of electrophoresis were developed using intact DNA molecules from the bacterial viruses lambda, T4 and G. Their DNAs have molecular weights (M) of 32 million, 120 million, and 500 million, respectively. Several electrophoresis conditions were found which give sufficiently high mobilities and large differences that these DNAs are separated in a short time. Electrophoresis in 0.1% agarose at 2.5 V/cm of gel length separates T4 and lambda DNAs by 2.0 cm, and G and T4 DNAs by 1.0 cm in only 10 hr. With some conditions DNA mobilities are directly proportional to log M for M values from 10 to 500 million. The procedures used will allow rapid molecular weight determination and separation of very large DNA molecules.

Bacillus megaterium↗

PubMed2003

Manual 768 or 384 well microplate gel 'dry' electrophoresis for PCR checking and SNP genotyping.

Electrophoresis continues to be a mainstay in molecular genetic laboratories for checking, sizing and separating both PCR products, nucleic acids derived from in vivo or in vitro sources and nucleic acid-protein complexes. Many genomic and genetic applications demand high throughput, such as the checking of amplification products from many loci, from many clones, from many cell lines or from many individuals at once. These applications include microarray resource development and expression analysis, genome mapping, library and DNA bank screening, mutagenesis experiments and single nucleotide polymorphism (SNP) genotyping. PCR hardware compatible with industry standard 96 and 384 well microplates is commonplace. We have previously described a simple system for submerged horizontal 96 and 192 well polyacrylamide or agarose microplate array diagonal gel electrophoresis (MADGE) which is microplate compatible and suitable for PCR checking, SNP typing (restriction fragment length polymorphism or amplification refractory mutation system), microsatellite sizing and identification of unknown mutations. By substantial redesign of format and operations, we have derived an efficient 'dry' gel system that enables direct 96 pin manual transfer from PCR or other reactions in microplates, into 768 or 384 well gels. Combined with direct electrode contact in clamshell electrophoresis boxes which plug directly to contacts in a powered stacking frame and using 5-10 min electrophoresis times, it would be possible (given a sufficient supply of PCRs for examination) for 1 million gel tracks to be run per day for a minimal hardware investment and at minimal reagent costs. Applications of this system for PCR checking and SNP genotyping are illustrated.

DNA↗