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At least 1,351 records · Page 75Linked to original sources
PubMed2005

Allele-specific transcript quantification detects haplotypic variation in the levels of the SDF-1 transcripts.

It has been suggested that SDF1-G801A, a single nucleotide polymorphism (SNP) in the 3' untranslated region (UTR) of the SDF1 gene, is associated with susceptibility to diseases such as AIDS and type-I diabetes. However, experimental studies examining the effect of SDF1-G801A on SDF-1 expression have not supported its functional importance. In this study, to examine whether other polymorphisms have a cis-acting effect on SDF1 expression, we carried out haplotype analyses of the SDF1 gene and the allele-specific transcript quantification utilizing Epstein-Barr virus-transformed lymphoblastoid cell lines with heterozygous genotype for SDF1-G801A. Haplotype-based analyses on the proportion of the allele-specific transcripts revealed the presence of haplotypes associated with a decreased amount of the transcripts. In addition, we observed haplotypic variation in response to dibutyl cyclic AMP and tetradecanoyl phorbol acetate that enhances the levels of SDF-1 transcripts probably through activation of transcription factors. Showing evidence that polymorphisms other than the SDF1-G801A have a cis-acting effect on expression of SDF-1 transcripts, the results of this study contribute to the interpretation of previous disease-association studies and to the selection of SNP markers for future studies. As shown in this study, allele-specific transcript quantification coupled with haplotype analyses can be an effective tool for detecting cis-acting polymorphisms in expressional regulation.

Alleles↗
PubMedDate not supplied

A polyvalent method using HPLC for screening and quantification of 12 common barbiturates in various biological materials.

A high-performance liquid chromatographic (HPLC) assay has been developed for the identification and quantification of 12 barbiturates at toxic and therapeutic levels in plasma, urine, gastric content, postmortem blood, and tissues. The sample preparation procedure involves a single-step extraction for plasma, urine, and gastric contents, and a supplementary back-extraction for postmortem blood and tissues. Appropriate internal standards are used for quantification. A mu Bondapak C18 column is used with a mobile phase of 40% methanol and (NH4)2HPO4 (0.05M). The barbiturates are detected at 240 and 290 nm. This method is rapid, sensitive, reproducible, relatively selective, and applicable to a great variety of biological fluids; it has been used regularly in forensic and clinical toxicological analyses.

Barbiturates↗
PubMedDate not supplied

Quantification of the putative neurotoxin 2-amino-3-(methylamino)propanoic acid (BMAA) in cycadales: analysis of the seeds of some members of the family Cycadaceae.

Over the past 30 years there have been attempts to link the unusually high incidence of amyotrophic lateral sclerosis (ALS) among the Chamorros native to the island of Guam to the consumption of the seeds of Cycas circinalis L., the false sago palm. In support of this relationship it was recently shown that, when given to primates, 2-amino-3-(methylamino)-propanoic acid (BMAA), a minor cycad component, can cause selective degeneration of upper and lower motor neurons in the spinal cord and clinical features similar to those of ALS. In order to test the relationship between ALS and cycads, we have developed a sensitive and precise gas chromatographic/mass spectrometric (GC/MS) assay for BMAA which allows direct assessment of the BMAA content in foods and is directly applicable to the assay of BMAA in biologic tissues and fluids. After the addition of a deuterated isotopomer as an internal standard and transesterication with 2-methyl-1-propanol, BMAA was extracted into dichloromethane and then acylated with pentafluoropropionic anhydride before GC/MS. This method permits precise quantification of BMAA in the low picogram/sample range. Direct quantification of the BMAA content in the female gametophyte tissue (endosperm) of a range of cycad seeds collected from Guam confirmed the presence of BMAA at levels of approximately 1 g/g (dry weight). The presence of BMAA in the seed extract was confirmed after derivatization of an aliquot of the extract and GC/MS analysis in the scanning mode. BMAA was found to be present, albeit at lower levels, in the endosperm of the seeds of C. revoluta (0.32 mg/g) and C. media (0.29 mg/g).

Amino Acids, Diamino↗
PubMedDate not supplied

Evaluation of the Coat-A-Count 125I fentanyl RIA: comparison of 125I RIA and GC/MS-SIM for quantification of fentanyl in case urine specimens.

The Coat-A-Count solid phase 125I Fentanyl Radioimmunoassay was evaluated with respect to linearity and precision using equine urine fortified with fentanyl and then compared with a gas chromatographic/mass spectrometric method for quantification of fentanyl in urine. The RIA assay was found to be linear over the urine fentanyl concentration range of 0.25 to 7.5 ng/mL and precise with coefficients of variation (CV) ranging from 9.6 to 19.3%. The RIA calibrators, ranging in fentanyl concentrations from 0.25 to 7.5 ng/mL, and controls, at mean fentanyl concentrations of 0.46 and 1.32 ng/mL, were compared by both the RIA and GC/MS methods. The cross-reactivity with the 125I RIA test was determined for the fentanyl metabolites, norfentanyl and hydroxyfentanyl, and found to be 5% and 35%, respectively. The illicit fentanyl analogs were found to show significant cross-reactivity, ranging from 20 to 100%. The 125I RIA was compared to GC/MS quantifications of fentanyl in 35 positive and 20 negative case urine specimens.

Cross Reactions↗
PubMedDate not supplied

Fast quantification of ethanol in whole blood specimens by the enzymatic alcohol dehydrogenase method. Optimization by experimental design.

A sensitive, fast, simple, and high-throughput enzymatic method for the quantification of ethanol in whole blood (blood) on Hitachi 917 is presented. Alcohol dehydrogenase (ADH) oxidizes ethanol to acetaldehyde using the coenzyme nicotinamide adenine dinucleotide (NAD), which is concurrently reduced to form NADH. Method development was performed with the aid of factorial design, varying pH, and concentrations of NAD+ and ADH. The linear range increased and reaction end point decreased with increasing NAD+ concentration and pH. The method was linear in the concentration range 0.0024-0.4220 g/dL. The limits of detection and quantification were 0.0007 g/dL and 0.0024 g/dL, respectively. Relative standard deviations for the repeatability and within-laboratory reproducibility were in the ranges 0.7-5.7% and 1.6-8.9%, respectively. The correlation coefficient when compared with headspace gas chromatography-flame ionization detection methods was 0.9903. Analysis of authentic positive blood specimens gave results that were slightly lower than those of the reference method.

Alcohol Dehydrogenase↗
PubMed2005

Quantification of ricinine in rat and human urine: a biomarker for ricin exposure.

Ricin is a toxalbumin derived from the castor bean plant, Ricinus communis. Ricinine is an alkaloid (3-cyano-4-methoxy-N-methyl-2-pyridone) that shares a common plant source with ricin, and its presence in urine infers ricin exposure. A new quantification method for ricinine was developed that uses solid-phase extraction to prepare 1-mL urine samples (81% recovery) for a 5-min, isocratic high-performance liquid chromatography method, followed by electrospray ionization tandem mass spectrometry. Protonated molecular ions were selected in the multiple reaction monitoring mode and quantified by isotope dilution with (13)C(6)-labelled ricinine as the internal reference. Urine pools enriched with ricinine at two concentrations were characterized as quality control materials and then used to validate the method. The method limit of quantification was 0.083 ng/mL, even with a confirmation ion of low relative abundance. Ricinine was stable in human urine when heated at 90 degrees C for 1 h, and during storage at 25 degrees C and 5 degrees C for 3 weeks. The method was applied to an animal exposure study, a crude ricin preparation scheme, and a forensic analysis. These studies show that ricinine can be measured in rat urine at least 48 h after exposure. Ricinine is present in crude preparations of ricin, and it can be found in human urine after a lethal exposure to ricin.

Alkaloids↗
PubMedDate not supplied

An automated alcohol dehydrogenase method for ethanol quantification in urine and whole blood.

In a previous work, an automated alcohol dehydrogenase method for the quantification of ethanol in whole blood (blood) specimens was presented. In the present work the application of the method to urine specimens has been investigated. Also, method robustness to routine analysis of urine and blood specimens during a period of eight months is shown. The limits of detection and quantification for urine were 0.0012 g/dL and 0.0042 g/dL, respectively. Relative standard deviations for the repeatability and within-laboratory reproducibility were in the ranges 1.4-4.1% and 1.8-4.6%, respectively. The method was compared with two headspace gas chromatography-flame ionization detection methods using authentic forensic urine specimens (n = 305) and blood specimens (n = 3186). Passing-Bablok regression for the concentration range 0.01-0.48 g/dL (urine) and 0.002-0.40 g/dL (blood) showed a statistically significant difference, for urine y = 0.9313 (0.9250 - 0.9377)x + 0.0038 (0.0029-0.0044) and for blood y = 0.9493 (0.9491 - 0.9495)x + 0.0032 (0.00318-0.00323), at 95% confidence level. The results of the external quality control specimens were in accordance with the reported theoretical concentrations.

Alcohol Dehydrogenase↗
PubMed2005

Rapid quantification of urinary 11-nor-delta9-tetrahydrocannabinol-9-carboxylic acid using fast gas chromatography-mass spectrometry.

Human urine specimens that were determined to be presumptively positive for metabolites of delta9-tetrahydrocannabinol by immunoassay screening were assayed using a novel fast gas chromatography-mass spectrometry (FGC-MS) analytical method to determine whether this method would improve the efficiency of specimen processing without diminishing the reliability of metabolite identification and quantification. Urine specimens were spiked with deuterated internal standard, subjected to solid-phase extraction, and derivatized using tetramethylammonium hydroxide and iodomethane. The methyl ester/methyl ether derivatives were identified and quantified using both a traditional GC-MS method and the newly developed FGC-MS method. The FGC-MS method was demonstrated to be linear between 3.8 and 1500 ng/mL 11-nor-delta9-tetrahydrocannabinol-9-carboxylic acid (11-nor-delta-THC-COOH). The intrarun precision of 15 replicates of a 15 ng/mL control and the interrun precision of 161 sets of 7, 15, and 60 ng/mL controls were acceptable (coefficients of variation < 5.5%). The FGC-MS method was demonstrated to be specific for identifying 11-nor-delta9-THC-COOH and none of 43 tested substances interfered with identification and quantification of 11-nor-delta9-THC-COOH. Excellent data concordance (R2 > 0.993) was found for two specimen sets assayed using both methods. The FGC-MS method, when compared with a traditional GC-MS method, reduces total assay time by approximately 40% with no decrease in data quality.

Dronabinol↗
PubMed2006

Quantification of metaxalone in human plasma by liquid chromatography coupled to tandem mass spectrometry.

A simple, rapid, sensitive, and selective liquid chromatography-tandem mass spectrometry (MS) method was developed and validated for the quantification of metaxalone, a skeletal muscle relaxant, in human plasma using galantamine as internal standard (IS). Following liquid-liquid extraction, the analytes were separated using an isocratic mobile phase on a reverse phase C18 column and analyzed by MS in the multiple reaction monitoring mode using the respective [M+H]+ ions, m/z 222/161 for metaxalone and m/z 288/213 for the IS. The assay exhibited a linear dynamic range of 50-5000 microg/L for metaxalone in human plasma. The lower limit of quantification was 50 microg/L with a relative standard deviation of less than 10%. Acceptable precision and accuracy were obtained for concentrations over the standard curve range. A run time of 2.5 min for each sample made it possible to analyze more than 400 human plasma samples per day. The validated method has been successfully used to analyze human plasma samples for application in pharmacokinetic, bioavailability, or bioequivalence studies.

Chromatography, High Pressure Liquid↗
PubMed1989

Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY).

The polymerase chain reaction (PCR) is used as part of a new approach to the absolute quantification of mRNA. We describe a PCR aided transcript titration assay (PATTY) which is based on the co-amplification of an in vitro generated transcript differing by a single base exchange from the target mRNA. Identical portions of a total RNA sample are "spiked" with different amounts of this mutated standard RNA, converted to cDNA and amplified by PCR. Because the base exchange creates a novel restriction endonuclease site, the ratio of co-amplified DNA derived from target mRNA to amplified DNA derived from standard RNA can be determined after restriction endonuclease digestion and separation by gel electrophoresis. This method gives accurate results within 24 hours and is useful especially for the quantification of either low-abundance mRNA or more abundant mRNA present in very small amounts of total RNA. The low-abundance mRNA encoding 4-coumarate:CoA ligase (4CL) in cultured potato cells (Solanum tuberosum L.) was measured in a case study. About 100 molecules per assay could be accurately detected by the new method.

Base Sequence↗
PubMed2000

A method for quantification of absolute amounts of nucleic acids by (RT)-PCR and a new mathematical model for data analysis.

Accurate quantification of nucleic acids by competitive (RT)-PCR requires a valid internal standard, a reference for data normalization and an adequate mathematical model for data analysis. We report here an effective procedure for the generation of homologous RNA internal standards and a strategy for synthesizing and using a reference target RNA in quantification of absolute amounts of nucleic acids. Further, a new mathematical model describing the general kinetic features of competitive PCR was developed. The model extends the validity of quantitative competitive (RT)-PCR beyond the exponential phase. The new method eliminates the errors arising from different amplification efficiencies of the co-amplified sequences and from heteroduplex formation in the system. The high accuracy (relative error <2%) is comparable to the recently developed real time detection 5'-nuclease PCR. Also, corresponding computer software has been devised for practical data analysis.

Cell Line↗
PubMed2001

Quantification of splice variants using real-time PCR.

A reliable and robust method for measuring the expression of alternatively spliced transcripts is an important step in investigating the significance of each variant. So far, accurate quantification of splice variants has been laborious and difficult due to the intrinsic limitations of conventional methods. The many advantages of real-time PCR have made this technique attractive to study its application in quantification of splice isoforms. We use skipping of exon 37 in the NF1 gene as a model to compare and evaluate the different strategies for quantitating splice variants using real-time PCR. An overview of three different possibilities for detecting alternative transcripts is given. We propose the use of a boundary-spanning primer to quantify isoforms that differ greatly in abundance. We describe here a novel method for creating a reliable standard curve using one plasmid containing both alternative transcripts. In addition, we validate the use of an absolute standard curve based on a dilution series of fluorometrically quantified PCR products.

Alternative Splicing↗
PubMed2002

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification.

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down's syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50-70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences.

Adaptor Proteins, Signal Transducing↗
PubMed2002

T7 RNA polymerase as a self-replicating label for antigen quantification.

Enzymes are used widely as labels in binding assays for protein analytes, because they provide signal amplification. Efforts at improving the assay sensitivity have been focused mainly on the synthesis of novel substrates, e.g. fluorogenic and chemiluminogenic ones. We report the investigation of T7 RNA polymerase (T7RP) as a label with unique characteristics for antigen quantification. In an in vitro, coupled (one-step) transcription/translation reaction, T7RP catalyzes the expression of an enzyme-coding DNA template to produce free enzyme (luciferase) in solution. We demonstrate that the generated luciferase is linearly related to the input T7RP in a range covering over four orders of magnitude. It is also shown that T7RP exhibits a significant level of self-replication (100-fold) in vitro by acting on a DNA template comprising the T7RP cDNA downstream of a T7 promoter. By combining the self-replication reaction with the expression of luciferase DNA, as low as 1400 T7RP molecules are detectable. Furthermore, the T7RP is biotinylated, complexed with streptavidin and used for antigen quantification in a microtiter well-based assay with high sensitivity and reproducibility.

Biotinylation↗
PubMed2003

Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments.

DNA quantification of soils and sediments is useful for the investigation of microbial communities and for the acquisition of their genomes that are exploited for the production of natural products. However, in such samples DNA quantification is impaired by humic acids (HA). Due to its lack of specificity and sensitivity, UV spectrophotometry cannot be applied. Consequently, fluorimetric assays applying Hoechst (H) 33258 or PicoGreen (PG) are used. Here, we investigated the SYBR Green I (SG) assay, which was also affected by HA, but was found to be 25- and 1.7-fold more sensitive compared to the H 33258 and PG assays, respectively. Spectrophotometric, fluorimetric and quenching studies as well as gel mobility shift assays suggested that the effect of HA on the SG assay was based on an inner filter effect, collisional quenching and binding of SG to HA. As to the latter finding, the standard 6250-fold dilution of the SG reagent was optimised to a 2000-fold dilution. Although the sensitivity of the optimised SG assay was reduced by a factor of 1.3, the interfering effect of HA could be reduced up to 22-fold. A significant reduction of HA interferences by lowering the pH of the assay was not observed. Finally, the performance of the modified SG assay and the corresponding evaluation methods were verified by the determination of DNA recoveries and concentrations of standards and environmental samples in comparison to the PG assay.

Benzothiazoles↗
PubMed2003

Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry.

As the DNA sequence of the human genome is now nearly finished, the main task of genome research is to elucidate gene function and regulation. DNA methylation is of particular importance for gene regulation and is strongly implicated in the development of cancer. Even minor changes in the degree of methylation can have severe consequences. An accurate quantification of the methylation status at any given position of the genome is a powerful diagnostic indicator. Here we present the first assay for the analysis and precise quantification of methylation on CpG positions in simplex and multiplex reactions based on matrix-assisted laser desorption/ ionisation mass spectrometry detection. Calibration curves for CpGs in two genes were established and an algorithm was developed to account for systematic fluctuations. Regression analysis gave R(2) >or= 0.99 and standard deviation around 2% for the different positions. The limit of detection was approximately 5% for the minor isomer. Calibrations showed no significant differences when carried out as simplex or multiplex analyses. All variable parameters were thoroughly investigated, several paraffin-embedded tissue biopsies were analysed and results were verified by established methods like analysis of cloned material. Mass spectrometric results were also compared to chip hybridisation.

Base Sequence↗
PubMed2004

A novel technique based on a PNA hybridization probe and FRET principle for quantification of mutant genotype in fibrous dysplasia/McCune-Albright syndrome.

Somatic mutations are present in various proportions in numerous developmental pathologies. Somatic activating missense mutations of the GNAS gene encoding the Gs(alpha) protein have previously been shown to be the cause of fibrous dysplasia of bone (FD)/McCune-Albright syndrome (MAS). Because in MAS patients, tissues as diverse as melanocytes, gonads and bone are affected, it is generally accepted that the GNAS mutation in this disease must have occurred early in development. Interestingly, it has been shown that the development of an active FD lesion may require both normal and mutant cells. Studies of the somatic mosaic states of FD/MAS and many other somatic diseases need an accurate method to determine the ratio of mutant to normal cells in a given tissue. A new method for quantification of the mutant:normal ratio of cells using a PNA hybridization probe-based FRET technique was developed. This novel technique, with a linear sensitivity of 2.5% mutant alleles, was used to detect the percentage mutant cells in a number of tissue and cell culture samples derived from FD/MAS lesions and could easily be adapted for the quantification of mutations in a large spectrum of diseases including cancer.

Alleles↗
PubMed2004

Simple and accurate quantification of dialysis in acute renal failure patients during either urea non-steady state or treatment with irregular or continuous schedules.

BACKGROUND: The quantification of dialysis in critically ill acute renal failure (ARF) patients requires a unifying expression that can establish kinetic equivalence amongst patients treated with irregular or frequent intermittent haemodialysis (IHD) schedules or with differing renal replacement therapies. EKRjc is a generalized form of the equivalent urea renal clearance (EKRc), and represents the equivalent continuous urea clearance that will result in the given time-averaged concentration of urea, for the given amount of urea removal. The suitability of EKRjc for the measurement of dialysis dose in this setting is examined. SUBJECTS AND METHODS: 420 weeks of renal replacement therapy (IHD and continuous renal replacement therapy) were simulated in 15 virtual 'patients' using a variable volume double pool urea kinetic model. Additional data from eight ARF patients were used to exemplify calculations. 1260 EKRjc values were calculated using both formal urea kinetic modelling, as well as a simplified method that requires input of changes in patient fluid state and blood urea nitrogen concentrations over a period of observation, in addition to an initial estimate of patient post-dialysis urea distribution volume (V(T)). RESULTS: EKRjc is shown to provide a unifying expression of dialysis dose irrespective of IHD schedule or renal replacement therapy. EKRjc is shown to be independent from the assumption of the urea steady state, and intrinsically normalized to patient urea distribution volume to allow dose comparisons between patients of different size. Residual renal urea clearance is easily incorporated where present. EKRjc is easily calculated using the simplified method without the need for iterative urea kinetic modelling. The accuracy of this simplified method is maintained when the initial estimation of V(T) is both 25% greater or smaller than the true value. Calculation of EKRjc is exemplified using the clinical data. CONCLUSIONS: EKRjc is the most suitable urea kinetic expression for the quantification of dialysis in critically ill ARF patients.

Acute Kidney Injury↗