Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “sample preparation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources

[Evaluation of sensitivity of PCR for detecting DNA of Trypanosoma vivax with several methods of blood sample preparations].

Parasitological techniques show a low sensitivity for diagnosis of active infections with Trypanosoma sp. in livestock, particularly in the case of chronic infections. T. vivax antigen detection through antigen-ELISA developed by Nantulya and Lindqvist (1989) is not sensitive and specific enough for infection diagnosis. T. vivax DNA detection through polymerase chain reaction (PCR) using the oligonucleotides developed by MASIGA et coll. (1992) appears to be an alternative for a specific diagnosis of T. vivax active infections in livestock. Twenty-two blood samples containing known numbers of T. vivax/ml, ranging from 1 to 1767, were prepared by dilution of T. vivax infected sheep blood into blood from a non infected sheep. PCR sensitivity was evaluated in several types of blood sample preparations: crude heparinized blood, plasma, lysed blood, buffy coat from haematocrit capillary tubes, pellet from plasma centrifugation, and DNA purified with an ion exchange resin commercial kit. Crude heparinized blood almost always inhibited PCR. Sensitivity of PCR with plasma and lysed blood was low, around 450 parasites/ml. PCR on buffy coat was more sensitive, but PCR products were sometimes little visible. Pellet of plasma centrifugation is an original, fast and economic preparation, whose PCR products are highly visible and which presents a high sensitivity: one hundred percent of the samples were positive when the parasitaemia was over 9 parasites/ml. DNA purification is slightly more time consuming and expensive, since it requires several manipulations and the use of a commercial kit, but it appears to be the most sensitive technique among those investigated: one hundred percent of the samples were positive when the parasitaemia was over 2 parasites/ml; however, PCR products were sometimes difficult to interpret. These last two techniques are recommended for a sensitive and species-specific diagnosis of active infections of livestock with T. vivax. These techniques should be evaluated for other pathogenic trypanosome species of livestock.

Animals↗

Automated sample preparation and chromatographic analysis: determination of CGS 10787B and related compounds.

An automated method is described for analyzing biological samples originating from CGS 10787B drug disposition studies. The method incorporates a laboratory robot to prepare plasma and urine samples and a high performance liquid chromatographic system to simultaneously analyze for CGS 10787B, as well as metabolites and drug-related compounds (CGS 12094, CGS 17000, and CGS 17001). The robot allquots the biological sample, adds an internal standard, and performs all the steps necessary for the liquid-liquid extraction and concentration of the drug and related components, while operating unattended around the clock. Recovery and reproducibility assessments indicate good accuracy and precision for the method. The limits of detection for the method are 0.2 microgram/mL in plasma and 0.5 microgram/mL in urine, for all components.

Biotransformation↗

Comparison of variability associated with sample preparation in two-dimensional gel electrophoresis of cardiac tissue.

Variability is a major complicating factor in analysis by two-dimensional gel electrophoresis. Improvements in methodologies have focused on improving individual gel quality rather than reproducibility. We homogenized rat cardiac tissue and rehydrated using a matrix of buffers to determine the optimal sample conditions. Six buffers were used to solubilize the proteins. Solubilized proteins were separated by isoelectric focusing using four buffers. Gels were run in triplicate to assess the method of preparation yielding the least variability. Number of spots and variability were different between conditions. Proteins solubilized in a buffer containing 5 M urea, 2 M thiourea, 2% CHAPS, 2% SB 3-10, ampholytes, DTT, and protease inhibitors and focused in a buffer containing 9 M urea and 4% NP40 had the lowest coefficient of variation. Variability was compared across isoelectric point ranges and was different. Minimizing technical variability in two-dimensional polyacrylamide gel electrophoresis is critical to identify differences between conditions. Sample preparation should be optimized to minimize variability as well as to maximize the number of spots seen.

Animals↗

Reduction of animal usage by serial bleeding of mice for pharmacokinetic studies: application of robotic sample preparation and fast liquid chromatography-mass spectrometry.

Typically, pharmacokinetic studies in mice require one animal per time point, thus resulting in differences due to dosing error, animal to animal variation and more importantly the euthanasia of a large number of animals. A method for the determination of pharmacokinetic data from serially bled mice to support early drug discovery is described. Sample analysis relies on liquid chromatography coupled with tandem mass spectrometry permitting robust and reproducible analysis requiring approximately 3 min per sample. Several parameters are discussed including the method of sample collection, preparation and analysis. The use of serially bled mice has lead to a remarkable reduction in animal usage and a corresponding reduction in compound required for such experiments. Using conventional methodology, a nine-point pharmacokinetic curve with four animals per time point would require 36 mice. With the method described below, only four mice in total are used and euthanasia is not required, permitting reuse after several weeks recovery and washout. Also, pharmacodynamic-pharmacokinetic correlation is possible and is demonstrated using a mouse model of diabetes.

Animals↗

An automated analytical method for the determination of felbamate in human plasma by robotic sample preparation and reversed-phase high performance liquid chromatography.

An automated analytical method for the determination of felbamate in human plasma is described. Sample cleanup and preparation was performed by means of a Zymate II laboratory robot and consisted of a liquid-liquid extraction of felbamate and the internal standard, primidone, from human plasma to dichloromethane. The dichloromethane was evaporated and reconstituted in a phosphate buffer. Separation was performed by reversed-phase high performance liquid chromatography using a 5 microns Hypersil ODS column (150 x 4.6 mm) and a mobile phase consisting of a mixture of phosphate buffer (pH = 6.5, 0.015 M) and acetonitrile (79:21, v/v). Quantitation was performed by measurement of the UV absorbance at a wavelength of 210 nm. The lower limit of quantitation was 0.100 micrograms ml-1 using 200 microliters of plasma. The mean absolute analytical recovery of felbamate was 75.2% (n = 28). The recovery of the internal standard, primidone was 74.7% (n = 10). The within-day precision was below 3.8% at all concentration levels, except at the lower limit of quantitation (18.3%). The within-day accuracy varied between -3.7 and +7.4%. The between-day precision was below 5.0% at all concentration levels. The between-day accuracy of the method varied between -5.7 and +1.6%. The selectivity of the method towards several other anti-epileptic drugs has been demonstrated.

Anticonvulsants↗

New technique of sample preparation for respirometry of filamentous fungi.

Various difficulties in the respirometry of filamentous fungi were avoided by using samples of moist mycelium layered thinly on tantalum grids. A variety of measurements is feasible with such preparations and are illustrated with samples of Schizophyllum commune from liquid and solid cultures.

Basidiomycota↗

Influence of sample preparation, staining procedure and analysis conditions on bull sperm head morphometry using the morphology analyser integrated visual optical system.

The importance of standardizing the procedures of sample and slide preparation for computer-assisted morphologic analysis has been emphasized in human and veterinary andrology. The purpose of this study was to optimize slide preparation (dilution grade and sperm washing), staining procedures and analysis conditions (colour of light source and objective magnification) for the morphometric analysis of bull spermatozoa using the Hamilton Thorne morphology analyzer integrated visual optical system (IVOS). For experiment 1, one ejaculate was collected from one bull and diluted to 200,000-300,000 spermatozoa/microl. Slides were prepared and stained using seven different procedures: rapid Papanicolaou (PAP), rapid Papanicolaou with prolonged staining times (PAP+). Diff-Quik (DIF), haematoxylin (HEM). Farelly (FAR), Spermac (SPER) and the modified GZIN (MGZIN) staining. All slides were analysed using a Hamilton Thorne Morphology Analyser IVOS equipped alternatively with a red, green or blue light source, and a 40x or 100x oil immersion objective. Recognition and digitization errors as well as morphometric parameters were determined. The IVOS was unable to detect DIF-stained spermatozoa. The GZIN and the SPER staining as well as the blue light source led to unsatisfactory results. Among the staining methods examined, the FAR, HEM, PAP+, and PAP staining, preferably in combination with the green light source, and the 40x objective yielded optimal results concerning sperm recognition and digitization. The 100x objective did not allow reliable analysis of the sperm heads because of a frequently appearing digitization error. For experiment 2, three ejaculates were collected from each of three bulls and diluted to five dilution grades (100 000-500 000 spermatozoa/microl). An aliquot of each dilution grade was washed additionally. The percentage of correctly digitized sperm heads decreased with increasing spermatozoal concentration. However, the evaluation speed increased. The range of 200 000-300 000 spermatozoa/microl appeared to be a reasonable compromise for both criteria. Sperm washing failed to further improve the analysis results. Sperm head dimensions were influenced significantly by all variations of the methods in both experiments. In conclusion, using the proposed methods, the IVOS allows precise and reliable morphometric analyses of bull spermatozoa. The consistent application of these procedures may lead to an inter-laboratory standardization and to further establishment of generally accepted morphometric criteria used in human andrology (e.g. World Health Organisation or strict criteria).

Animals↗

A rapid sample preparation technique for flow cytometric analysis of immunofluorescence allowing absolute enumeration of cell subpopulations.

A simple and rapid method was developed for immunofluorescence measurements of cells by flow cytometry which does not require washing procedures, permitting absolute enumeration of cell subpopulations. Peripheral blood cells were labeled with fluorescein and phycoerythrin conjugated monoclonal antibodies and the nucleic acid stain LDS-751. Distilled water was added following incubation to induce erythrocyte lysis by hypotonic shock. After lysis for 30 s the tonicity of the sample was increased followed by measurement on the flow cytometer. The leukocyte populations were clearly resolved in the correlation of forward and orthogonal light scattering. The immunofluorescence resolution of the labeled leukocytes was equivalent to NH4Cl and a commercial lysing preparation. Absolute number of leukocytes and percentage of leukocyte subpopulations determined with this procedure correlated well with the results obtained with a clinical hematology analyzer. Cell recovery and preservation of cellular characteristics of three different procedures for lysing the human erythrocytes were compared. The LDS-751 permitted the discrimination of intact cells from residual erythrocyte ghosts, platelets and damaged nucleated cells. A considerable loss of cells was found for both NH4Cl and commercial lysing solution; the samples prepared by NH4Cl lysing had a selective loss of lymphocyte subpopulations as compared with the other two techniques. In contrast to the two procedures in which multiple washing steps are involved, the no wash, hypotonic lysis procedure provided a means of obtaining absolute numbers of leukocyte subpopulations identified by combining light scattering and immunofluorescence characteristics with no centrifugation steps required.

Ammonium Chloride↗

Interference and blood sample preparation for a pyruvate enzymatic assay.

BACKGROUND: To assess the severity of circulatory failure, a pyruvate enzymatic assay was performed on whole blood using lactate dehydrogenase to catalyze the conversion of pyruvate to lactate. We investigated factors related to blood sample collection and preparation that might influence the results, including the timing of blood deproteinization, temperature of sample storage, and hemolysis. METHOD: A total of 25 whole blood specimens were collected for this study. Each sample was divided into 2 parts: one stored at room temperature (RT) and another kept on ice. The samples were deproteinizied by using 8% perchloric acid (PCA) at varying times after collection; the first deproteinization was immediately after the blood was drawn (0 h), then at 1 h intervals for 6 h and also in samples kept overnight. The supernatant samples were analyzed soon after deproteinization using a COBAS Centrifugal Analyzer. In another set of samples, the blood was immediately deproteinized, and the supernatants were stored at RT and 4 degrees C and assayed for pyruvate at varying times, as above. Finally, the effect of hemolysis on the blood pyruvate enzymatic assay was also evaluated. RESULTS: When samples were stored at RT, pyruvate levels remained constant until the third h after deproteinization, when there was an approximately 13.3% increase in pyruvate concentration. When whole blood samples were kept at 4 degrees C before deproteinization, pyruvate levels were significantly reduced over time, ranging from 37.8% to 62.2% (paired t test showed a significant mean difference, P < 0.001). No significant differences in pyruvate concentration were observed in supernatant stored at either RT or 4 degrees C. Hemolysis caused a 33.7% increase in the pyruvate concentration, equivalent to 0.18 mg pyruvate per gram per deciliter of hemoglobin. CONCLUSIONS: For a pyruvate enzymatic assay, keeping a whole blood sample at RT will not cause a significant difference in the pyruvate level as long as the sample is immediately deproteinized. Whole blood samples should not be stored in an ice bath for transport, nor should hemolyzed samples be used for a blood pyruvate enzymatic assay.

Adult↗

Comparison of sample preparation methods for ChIP-chip assays.

A single chromatin immunoprecipitation (ChIP) sample does not provide enough DNA for hybridization to a genomic tiling array. A commonly used technique for amplifying the DNA obtained from ChIP assays is ligation-mediated PCR (LM-PCR). However; using this amplification method, we could not identify Oct4 binding sites on genomic tiling arrays representing 1% of the human genome (ENCODE arrays). In contrast, hybridization of a pool of 10 ChIP samples to the arrays produced reproducible binding patterns and low background signals. However the pooling method would greatly increase the number of ChIP reactions needed to analyze the entire human genome. Therefore, we have adapted the GenomePlex whole genome amplification (WGA) method for use in ChIP-chip assays; detailed ChIP and amplification protocols used for these analyses are provided as supplementary material. When applied to ENCODE arrays, the products prepared using this new method resulted in an Oct4 binding pattern similar to that from the pooled Oct4 ChIP samples. Importantly, the signal-to-noise ratio using the GenomePlex WGA method is superior to the LM-PCR amplification method.

Animals↗

False-positive results of plasma PCR for cytomegalovirus DNA due to delayed sample preparation.

Positive results by cytomegalovirus (CMV) PCR of plasma are considered predictive of active CMV infection in kidney allograft recipients. To assess whether contamination with leukocyte-derived CMV DNA can distort the results, aliquots of whole-blood samples from 60 CMV immunoglobulin G-positive patients with leukocyte CMV DNAemia were stored for up to 24 h at room temperature (RT) and at 4 degrees C before plasma preparation. Native and ultrafiltered plasma samples were tested by CMV and beta-globin PCRs. Among 30 latently infected patients (negative for CMV pp65 antigens), low baseline rates (10%) and levels (median number of copies, 10 [per 10 microl]) of CMV plasma DNAemia in native plasma samples increased significantly over time (after 4 h at RT, 37% [P < 0.001]; median number of copies, 45 [P < 0.001]). Similar effects were found during storage at 4 degrees C. Ultrafiltration reduced the levels of CMV plasma DNAemia, but by 6 h of storage the levels were significantly elevated as well. CMV and beta-globin DNA kinetics in plasma were parallel. In contrast, 30 actively infected patients (pp65 positive) had high baseline rates (87% in native samples) and levels (median number of copies, 75) of CMV plasma DNAemia. No significant effects of storage or ultrafiltration and no concordance with beta-globin DNA kinetics were seen. In conclusion, delayed preparation of plasma samples bears a significant risk of false-positive CMV PCR results, probably due to leukocyte lysis. This has important implications in the clinical setting and for PCR standardization.

Blood Specimen Collection↗

[A comparison of Fe, Zn, Cu, Cr, Cd and Pb concentration in serum determined by ICP-AES using different sample preparation procedures].

Fe, Zn, Cu, Cr, Cd and Pb concentrations in serum of 21 arteriosclerosis (AS) and 18 healthy control (CK) were determined by ICP-AES, and sample solution was prepared using acid digestion (Dig.) and acid dilution (Dil.) procedure. Serum total Fe, Zn and Cr were significantly higher using Dig. than that using Dil. Serum Cu and Pb were of no significant differences using the both procedures. Serum Cd was significantly lower using Dig. than that using Dil. The results of Fe, Cu, Zn and Cr were positively correlated between Dig. and Dil., but those of Pb and Cd were of no significant correlation. Six elements concentrations in serum determined were significantly different between AS and CK using Dig. The digestion procedure was recommended for serum trace elements analysis using ICP-AES.

Case-Control Studies↗

Microwave-assisted sample combustion: a technique for sample preparation in trace element determination.

A novel digestion procedure based on sample combustion ignited by microwave radiation is proposed for organic samples. Certified samples of bovine liver, pig kidney, and skim milk were used as examples to demonstrate the performance of the proposed procedure. Cadmium and copper were determined in these samples by electrothermal atomic absorption spectrometry. Samples (between 50 and 250 mg) were wrapped with paper and placed on a homemade quartz holder that was positioned inside to quartz vessels used in a commercial microwave oven. Ammonium nitrate solution was added to the paper, and vessels were pressurized with oxygen to 15 bar. The rotor containing four vessels was placed inside the oven, and microwave radiation was applied for 20 s at 1400 W. Combustion was complete in few seconds, and an additional reflux step, which was optional, was applied. The agreement to the certified values was between 96 and 105% for both analytes. Only with the combustion step, the residual carbon (RC) was below 1.3%. The RC decreased to less than 0.4% when an additional reflux step with concentrated nitric acid was applied.

Animals↗

Sample preparation methods for PCR detection of Escherichia coli O157:H7, Salmonella typhimurium, and Listeria monocytogenes on beef chuck shoulder using a single enrichment medium.

To improve the utility of the polymerase chain reaction (PCR) for food samples, methods for preparing template DNA were developed to remove PCR inhibitors. Beef chuck shoulder medallions, artificially contaminated, individually or in combination, with Escherichia coli serotype O157:H7 strain FSIS 45753-35, Salmonella typhimurium DT104 strain 13HP, or Listeria monocytogenes strain Scott A at concentrations of 10, 1 and 0.5 cfu/cm(2)were swabbed with a sponge, and the sponges were enriched for 18 h at 37 degrees C in universal pre-enrichment broth (UPB). Enriched broth cultures (EBC), cell pellets (CP), or phosphate-buffered saline-washed cell pellets (PBSCP) from enriched sponge samples were compared for detection of E. coli O157:H7, S. typhimurium DT104, or L. monocytogenes by the PCR using the BAX(TM)system. Recovery of the three organisms was effective for detection of each pathogen at initial levels of 10, 1 and 0.5 cfu/cm(2)when inoculated separately, or in combination, onto the beef samples. Use of EBC, CP, or PBSCP of sponge-swabbed samples eliminated problems associated with inhibition of the PCR by food components, time-consuming extraction of DNA, and inhibition due to large amounts of non-target DNA derived from the food. The procedure involving enrichment of sponge-swabbed beef samples in UPB followed by PCR amplification using EBC with the BAX system is the most efficient and simple method for detection of E. coli O157:H7, S. typhimurium DT104, and L. monocytogenes.

Animals↗

Development and evaluation of a micro- and nanoscale proteomic sample preparation method.

Challenges associated with the efficient and effective preparation of micro- and nanoscale (micro- and nanogram) clinical specimens for proteomic applications include the unmitigated sample losses that occur during the processing steps. Herein, we describe a simple "single-tube" preparation protocol appropriate for small proteomic samples using the organic cosolvent, trifluoroethanol (TFE) that circumvents the loss of sample by facilitating both protein extraction and protein denaturation without requiring a separate cleanup step. The performance of the TFE-based method was initially evaluated by comparisons to traditional detergent-based methods on relatively large scale sample processing using human breast cancer cells and mouse brain tissue. The results demonstrated that the TFE-based protocol provided comparable results to the traditional detergent-based protocols for larger, conventionally sized proteomic samples (>100 microg protein content), based on both sample recovery and numbers of peptide/protein identifications. The effectiveness of this protocol for micro- and nanoscale sample processing was then evaluated for the extraction of proteins/peptides and shown effective for small mouse brain tissue samples (approximately 30 microg total protein content) and also for samples of approximately 5000 MCF-7 human breast cancer cells (approximately 500 ng total protein content), where the detergent-based methods were ineffective due to losses during cleanup and transfer steps.

Animals↗

Automated analysis of oxolinic acid and flumequine in salmon whole blood and plasma using dialysis combined with trace enrichment as on-line sample preparation for high-performance liquid chromatography.

The use of dialysis as sample clean-up for high-performance liquid chromatography makes fully automated determination of drugs in whole blood and plasma possible. High recoveries of the analytes oxolinic acid and flumequine and the internal standard nalidixic acid are obtained after a short time of dialysis (7.3 min). The dilute dialysates are enriched on a small column packed with polystyrene. When dialysis is discontinued, the analytes are eluted by mobile phase to the analytical column. With UV detection the limit of detection was 50 ng/ml for both oxolinic acid and flumequine. Validation showed good precision and accuracy and good correlation between determinations in plasma and whole blood.

Animals↗

Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: sample preparation, data analysis, and application to the analysis of complex peptide mixtures.

We report the development of a robust interface for off-line coupling of nano liquid chromatography (LC) to matrix-assisted laser desorption/ionisation-mass spectrometry (MALDI-MS) and its application to the analysis of proteolytic digests of proteins, both isolated and in mixtures. The interface makes use of prestructured MALDI sample supports to concentrate the effluent to a small sample plate area and localize the MALDI sample to a predefined array, thereby enriching the analyte molecules and facilitating automated MALDI-MS analysis. Parameters that influence the preparation of MALDI samples from the LC effluent were evaluated with regard to detection sensitivity, spectra quality, and reproducibility of the method. A procedure for data processing is described. The presented nano LC MALDI-MS system allowed the detection of several peptides from a tryptic digest of bovine serum albumin, at analyzed amounts corresponding to one femtomole of the digested protein. For the identification of native proteins isolated from mouse brain by two-dimensional gel electrophoresis, nano LC MALDI-MS increased the number of detected peptides, thereby allowing identification of proteins that could not be identified by direct MALDI-MS analysis. The ability to identify proteins in complex mixtures was evaluated for the analysis of Escherichia coli 50S ribosomal subunit. Out of the 33 expected proteins, 30 were identified by MALDI tandem time of flight fragment ion fingerprinting.

Animals↗