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 469 records · Page 26Linked to original sources
PubMedDate not supplied

Intracellular detection of Bcl-2 and p53 proteins by flow cytometry: comparison of monoclonal antibodies and sample preparation protocols.

Several techniques have been proposed for flow cytometric evaluation of intracellular antigens. This approach is particularly important for detection at the single cell level of proteins which correlate to tumour progression. Bcl-2 and p53 are two of the most relevant proteins. In the present study we have compared five different cell fixation-permeabilisation protocols and nine fluorochrome-conjugated (FITC or PE) monoclonal antibodies (mAb): four mAb directed against Bcl-2 and five against p53. For detection of Bcl-2 we have analysed three Bcl-2 positive cell lines (K562, Daudi and MCF-7), and peripheral blood samples obtained from nine healthy subjects. To distinguish internal positive (lymphocytes) and negative control cells (granulocytes), it was necessary to perform simultaneous detection of surface and intracellular antigens. For detection of p53 three cell lines, two p53 positive (Raji and CEM) and one p53 negative (HL-60), were analysed. Using these cells we have performed a combined analysis of the efficiency of monoclonal antibodies and sample preparation techniques. In conclusion, clones 124-FITC and Bcl-2/100-PE (Bcl-2), and clones BP53,12-FITC and G59-12-PE (p53) provided the highest specific fluorescence intensity of the respective markers independent of cell preparation protocols. Importantly, our results show that mAb background may depend on the specific fixation/permeabilisation kit and that mAb titration using negative and positive control cells is essential to determine the specificity and the sensitivity of the mAb used.

Antibodies, Monoclonal↗
PubMed1994

[A practical method of whole mount TEM sample preparation and the study of nuclear matrix-intermediate filament scaffolds in K562 cells].

We applied culture plates with bored holes covered with FORMVAR and coated with carbon, to replace the gold grids used in conventional whole mount TEM study. Human erythroleukemia cell line K562 cells plated on the plate surface were extracted using a modified protocol to study scaffolds of nuclear matrix (NM) and intermediate filament (IF). The NM of the K562 cells was found to be composed of interweaving filaments of different diameters, while the cytoplasmic IF were mainly distributed in a radialized pattern. Compared with other techniques of whole mount TEM sample preparations, this one is much more practical and economical, yielding clear NM-IF structures with few artifacts. Study of NM-IF scaffolds in K562 cells might provide a basis for further elucidation of the involvement of NM-IF in the denucleation of mammalian erythroblasts.

Humans↗
PubMed1998

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for polymer analysis: solvent effect in sample preparation.

The success of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry for the characterization of polymer structures and for the determination of average molecular weights and distributions depends on the use of a proper sample/matrix preparation protocol. This work examines the effect of solvents, particularly solvent mixtures, used to prepare polymer, matrix, and cationization reagent solutions, on MALDI analysis. It is shown that the use of solvent mixtures consisting of polymer solvent does not have a significant effect on the molecular weight determination of polystyrene 7000 and poly(methyl methacrylate) 3750. However, solvent mixtures containing a polymer nonsolvent can affect the signal reproducibility and cause errors in average weight measurement. This solvent effect was further investigated by using confocal laser fluorescence microscopy in conjunction with the use of a fluorescein-labeled polystyrene. It is demonstrated that sample morphology and polymer distribution on the probe can be greatly influenced by the type of solvents used. For sample preparation in MALDI analysis of polymers, it is important to select a solvent system that will allow matrix crystallization to take place prior to polymer precipitation. The use of an excess amount of any polymer nonsolvent should be avoided.

Algorithms↗
PubMed1993

Sample preparation techniques.

Evidentiary false positives are caused by passive exposure to drugs in the environment rather than by active use of drugs. The avoidance of such positives is essential for both hair and urine analysis. Hair analysis enjoys the advantage over urinalysis in having a number of approaches for making this distinction. These include: methylene blue staining of the hair specimen for selecting the appropriate wash solvent; application of hair digestion techniques for the complete release of chemically unaltered analytes; the determination of three diagnostic ratios from wash and digestion data; the measurement of metabolite:drug ratios; the use of cut-off levels setting the limits for passive endogenous drug exposure; reproducibility of results (including segmental analysis) with a newly collected hair specimen; and the reporting of results as either negative, positive, or contaminated. Our sample preparation procedures have been effectively applied to the analyses of nearly 200,000 specimens, i.e. to approximately one million drug analyses for cocaine, opiates, methamphetamine, phencyclidine or marijuana. On the basis of this experience we conclude that hair analysis is a safe and effective method for workplace drug testing.

Aged↗
PubMed1988

Errors in bone blood flow measured with microspheres due to sample preparation technique.

An experiment was carried out to examine the effect of boiling the carcass on the subsequent microsphere content of the skeleton. Intracardiac injections of radioactive microspheres were made in five rabbits and the animals killed humanely. The tibia and femur were then removed from one lower limb by dissection, and from the other after boiling it in a pressure cooker. The mean radioactivity in the bones was significantly less following boiling: 61% (SD 14) of the control tibia and 56% (SD 11) of the control femur. As a methodological check, the radioactivity in the bones of left and right legs was compared after both had been removed by boiling. In three animals, the mean activity (left compared with right) was 101% (SD 6) in the tibia and 100% (SD 3) in the femur. Boiling the carcass led to a substantial reduction in the microsphere content of the bones and cannot be recommended as a method of sample preparation for quantitative bone blood flow work.

Animals↗
PubMed2000

On-line sample preparation using restricted-access media in the analysis of the soy isoflavones, genistein and daidzein, in rat serum using liquid chromatography electrospray mass spectrometry.

Soy isoflavones are the subject of many investigations in experimental animals and humans regarding possible modulation of endocrine activity and chemoprevention of carcinogenesis. Genistein and daidzein, the principal biologically active isoflavones in soy, were measured using on-line solid-phase extraction (SPE) and liquid chromatography electrospray mass spectrometry (LC/ES-MS) detection in serum of rats consuming a common open-formula (NIH 31) chow that contained approximately 30 microg each of genistein and daidzein per gram of feed and a specially designed 'soy-free' chow that contained approximately 60-fold lower isoflavones. The use of a restricted-access/reverse phase trap cartridge and automated column switching permitted rapid and robust analytical performance with many injections of plasma onto a reverse phase LC column. Enzymatic deconjugation and a single centrifugation step were the only sample preparation steps required. The limit of detection for the isoflavones, based on the MS responses observed in serum from male and female rats consuming the soy-free chow, was 0.020 microM. The method, which uses deuterated isoflavones as internal standards, was determined to be accurate using spiked control serum (102-110% of added amounts) and precise using spiked control serum and incurred serum (<6% relative standard deviation). The average genistein and daidzein levels were determined in female (0.62 and 0.25 microM, respectively) and male rats (0.35 and 0.20 microM, respectively) consuming the standard diet. The sex difference observed for serum genistein concentrations was statistically significant (p < 0.0001). These results underscore the potential impact of standard open-formula diets on the results from rodent bioassays of biological activity.

Animals↗
PubMed2006

Development of an enzyme-linked immunosorbent assay for fentanyl and applications of fentanyl antibody-coated nanoparticles for sample preparation.

A sensitive enzyme-linked immunosorbent assay (ELISA) was developed for the detection of fentanyl in serum and urine. The ELISA used an indirect competitive method produced by coating the plate with thyroglobulin conjugated with fentanyl hapten. Antibodies against fentanyl-hemocyanin were detected by a goat-anti-rabbit antibody conjugated with alkaline phosphatase. Calibration standard curves ranged from 0.5ng/ml to 50mug/ml (IC(50)=10ng/ml), and the limits of detection were 0.5 and 1.0ng/ml for serum and urine, respectively. The intra- and inter-assay variations were less than 8% and 10%, respectively. The antibody produced against fentanyl completely cross-reacted with p-fluorofentanyl, thienylfentanyl and 3-methylthienylfentanyl, cross-reacted highly with carfentanil (85%), but was considered non-cross-reactive with alpha-methylfentanyl (5%), sufentanil (<1%), alfentanil (<1%) and lofentanil (<1%). Nano-sized iron oxide magnetic particles coated with the developed fentanyl antibody were capable of specific binding and releasing of fentanyl from urine samples. This enabled the drug to be effectively pre-concentrated and decreased the limit of detection by approximately one order of magnitude. The analytical background noise was significantly reduced to enable fentanyl detection at concentrations originally below chromatographic limit of detection. The change of platform for antibody binding with nanoparticles demonstrated a novel use of antibodies for sample preparation and should facilitate drug screening by traditional ELISA.

Adjuvants, Anesthesia↗
PubMed2002

Proteoglycan and proteome profiling of central human pulmonary fibrotic tissue utilizing miniaturized sample preparation: a feasibility study.

The objective of this study was to isolate fibrotic cells from human lung biopsies taken from different central pulmonary locations. A comparison was made of cell morphology, proteoglycan- and protein-expression in mesenchymal cell cultures obtained from human bronchial biopsies from patients with asthmatic-like disorders. We isolated viable cells from 10 out of the 12 biopsies. The fibroblast-like cells were positive for the biomarker a-smooth muscle actin, indicating that the cells were in an activated state. Two different types of fibroblast-like cells were observed from human pulmonary connective tissue; one of contractile type with lamellipodia that facilitate migration and a second cell type with an increased cell size, which most likely is of a synthetic phenotype. This is the first evidence of alterations in the proteoglycan expression pattern of versican, perlecan, biglycan and decorin which can be linked to the pathophysiological state of asthmatics proven by a combination of solid-phase extraction by reversed phase and by peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Protein expression analysis using two-dimensional electrophoresis was interfaced to miniaturized sample preparation techniques using microcapillary extraction. Four protein groups were identified; cytoskeletal, adhesion, scavenger and metabolic proteins. These patient's proteomes showed a high degree of heterogeneity between patients but larger homogeneity within biopsies derived from different locations of the same patient.

Actins↗
PubMed2002

Determination of Cd and Pb in food slurries by GFAAS using cryogenic grinding for sample preparation.

A simple method combining slurry sampling after cryogenic grinding and the use of a permanent modification of the integrated platform inside the transversely heated graphite atomizer (THGA) was proposed for the determination of Cd and Pb in foods. Potentialities of the cryogenic grinding were evaluated for grinding different materials of difficult homogenization such as high fat and high fiber tissues. Animal and vegetal samples were cut into small pieces and ground in liquid nitrogen for 2 min. Slurries were prepared directly in the autosampler cup after cryogenic grinding by transferring an exact amount of homogeneous powdered material (5-20 mg) to the cup, followed by 1.00 mL of 0.2% (v/v) HNO3 containing 0.04% (v/v) Triton X-100 and sonication for 30 s, before transferring into the platform previously coated with 250 microg W and 200 microg Rh. Use of a tungsten carbide-rhodium permanent modifier combined with NH4H2PO4 conventional modifier improves tube lifetime and increases the pyrolysis temperature for Cd. Homogeneity tests, carried out by comparing the between- and within-batch precision for each kind of sample, showed no significant differences at the 95% confidence level, indicating good homogeneity for 5-20 mg masses. Detection limits were 3.3 ng g(-1) Cd and 75 ng g(-1) Pb for 1% m/v slurries. Results for determination of Cd and Pb in foods slurries were in agreement with those obtained with digested samples, since no statistical differences were found by the paired t-test at the 95% level.

Cadmium↗
PubMed2006

Automated sample preparation and analysis using a sequential-injection-capillary electrophoresis (SI-CE) interface.

A fully automated sequential-injection-capillary electrophoresis (SI-CE) system was developed using commercially available components as the syringe pump, the selection and injection valves and the high voltage power supply. The interface connecting the SI with the CE unit consisted of two T-pieces, where the capillary was inserted in one T-piece and a Pt electrode in the other (grounded) T-piece. By pressurising the whole system using a syringe pump, hydrodynamic injection was feasible. For characterisation, the system was applied to a mixture of adenosine and adenosine monophosphate at different concentrations. The calibration curve obtained gave a detection limit of 0.5 microg g(-1) (correlation coefficient of 0.997). The reproducibility of the injection was also assessed, resulting in a RSD value (5 injections) of 5.4%. The total time of analysis, from injection, conditioning and separation to cleaning the capillary again was 15 minutes. In another application, employing the full power of the automated SIA-CE system, myoglobin was mixed directly using the flow system with different concentrations of sodium dodecyl sulfate (SDS), a known denaturing agent. The different conformations obtained in this way were analysed with the CE system and a distinct shift in migration time and decreasing of the native peak of myoglobin (Mb) could be observed. The protein samples prepared were also analysed with off-line infrared spectroscopy (IR), confirming these results.

Journal Article↗
PubMed2006

Reduction of proteins during sample preparation and two-dimensional gel electrophoresis of woody plant samples.

Protein extraction procedure and the reducing agent content (DTT, dithioerythritol, tributyl phosphine and tris (2-carboxyethyl) phosphine (TCEP)) of the sample and rehydration buffers were optimised for European beech leaves and roots and Norway spruce needles. Optimal extraction was achieved with 100 mM DTT for leaves and needles and a mixture of 2 mM TCEP and 50 mM DTT for roots. Performing IEF in buffers containing hydroxyethyldisulphide significantly enhanced the quality of separation for all proteins except for acidic root proteins, which were optimally focused in the same buffer as extracted.

Buffers↗
PubMed1982

Effect of sample preparation on analysis of superoxide dismutase activity and isoenzymes.

The effect of superoxide dismutase (SOD) activity and isoenzyme pattern of detergents, incubation time, and sonication in the preparation of rat liver samples was investigated. The activity of the manganese form of the enzyme (Mn-SOD) was found to decrease significantly after 4 hr of incubation at room temperature, and activity of the copper, zinc form of the enzyme (Cu, Zn-SOD) was not changed significantly even after 24 hr, although levels were somewhat decreased. Sonication of the sample did not affect Cu, Zn-SOD activity, but total Mn-SOD activity was increased. Addition of detergents did not increase Mn-SOD activity when homogenates were sonicated, indicating that Mn-SOD is not membrane bound. Detergents also had no effect on Cu, Zn-SOD activity. None of the treatments investigated altered the isoenzyme patterns, providing evidence that these isoenzymes are not degradation products.

Animals↗
PubMedDate not supplied

A robotic system to prepare samples for HTLV-III testing.

A robotic handling system was adapted to perform the sampling and dilution steps needed in an assay to detect antibodies to the HTLV-III virus, the causative agent of AIDS. The system reduced the labor required to prepare the samples and provided standardization and accuracy in the preparation of the samples.

Antibodies, Viral↗
PubMed2000

Saccharose solid matrix embedded proteins: a new method for sample preparation for X-ray absorption spectroscopy.

In this study, solid samples of hemoglobin and hemocyanin have been prepared by embedding the proteins into a saccharose-based matrix. These materials have been developed specifically for specimens for X-ray absorption spectroscopy (XAS). The preservation of protein conformation and active site organization was tested, making comparisons between the solid and the corresponding liquid samples, using resonance Raman, infra red, fluorescence and XAS. The XAS spectra of irradiated solid and liquid samples were then compared, and the preservation of biological activity of the proteins during both preparation procedure and X-ray irradiation was assessed. In all cases, the measurements clearly demonstrate that protein solid samples are both structurally and functionally quite well preserved, much better than those in the liquid state. The saccharose matrix provides an excellent protection against X-ray damages, allowing for longer exposure to the X-ray beam. Moreover, the demonstrated long-term stability of samples permits their preparation and storage in optimal conditions, allowing for the repetition of data collection with the same sample in several experimental sessions. The very high protein concentration that can be reached results in a significantly better signal-to-noise ratio, particularly useful for high molecular weight proteins with a low metal-to-protein ratio. On the bases of the above-mentioned results, we propose the new method as a standard procedure for the preparation of biological samples to be used for XAS spectroscopy.

Animals↗
PubMed1998

Utility of thin-layer preparations in thyroid fine-needle aspiration: diagnostic accuracy, cytomorphology, and optimal sample preparation.

BACKGROUND: The efficacy of preparing thyroid fine-needle aspirations (FNAs) as thin-layer slides has not been evaluated extensively. METHODS: To evaluate the efficacy of thin-layer cytology, the authors examined thyroid FNAs from 135 unselected palpable lesions that were aspirated using uniform procedures and prepared as air-dried, Diff-Quik-stained direct smears (DS) and Papanicolaou-stained thin-layer slides (TL). Diagnoses rendered independently on masked slides from each thyroid nodule were compared with the reported final cytologic or histologic diagnoses based on all available pathologic material. Slides were analyzed for diagnostically important cytologic features and the optimal number of TL slides per sample was assessed. RESULTS: TL diagnoses agreed with final diagnoses in 85% of cases compared with 96% for DS. All 11 neoplasms were recognized in both preparations. A final diagnosis of chronic lymphocytic thyroiditis (CLT) was missed in 10 of 26 TL (39%) compared with 2 of 26 DS (8%) (P = 0.013, McNemar's test). Cytologic features appreciated less often in TL than DS (McNemar's test) included diffuse colloid, spherules, tissue fragments, and lymphocytes. Multinucleated giant cells were identified more often in TL than DS. Two TL slides were sufficient for diagnosis in 83% of cases. CONCLUSIONS: The diagnostic accuracy of TL was 85% compared with 96% for DS. CLT was diagnosed accurately in 62% of TL compared with 92% of DS. Cytologic features in TL and DS may differ. Preparation of only two TL slides is adequate for definitive diagnosis in most cases.

Biopsy, Needle↗
PubMed2002

A highly reproducible, linear, and automated sample preparation method for DNA microarrays.

DNA microarrays are powerful tools to detect changes in transcript abundance in multiple samples in parallel. However, detection of differential transcript levels requires a reproducible sample (target) preparation method in addition to a high-performance microarray. Therefore, we optimized a target-preparation method that converts the poly(A)(+) RNA fraction of total RNA into complementary DNA, then generates biotin-labeled complementary RNA from the cDNA. We measured the efficiency of incorporation of biotin-containing nucleotides by an enzymatic digestion, followed by resolution via analytical high-performance liquid chromatography (HPLC). When the target was hybridized to a sensitive and reproducible microarray platform, low coefficients of variation in both hybridization intensities and differential expression ratios across target preparations were observed. Nearly identical hybridization intensities and expression ratios are observed regardless of whether poly(A)(+)-enriched RNA or total RNA is used as the starting material. We show the ability to discern biological and production variability through the use of different lots of commercial samples as visualized by hierarchical clustering. Automation of the target-preparation procedure shows equivalence to the manual procedure, reproducible yields of target, and low variability as measured by hybridization to microarrays. Most importantly, RNA mixing experiments show a linear and quantitative amplification in probe hybridization signals for >6000 genes across the entire signal range.

Biotinylation↗