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Wide variability in the sensitivity of APTT reagents for monitoring of heparin dosage.

AIM: To assess the sensitivity of activated partial thromboplastin time (APTT) reagents for monitoring heparin dosage using data from the UK National External Quality Assessment Scheme (NEQAS) for blood coagulation. METHODS: Data were reviewed from four surveys using samples prepared by addition of heparin to normal plasma in vitro and from two surveys in which samples were prepared using plasma from patients receiving heparin therapy (ex vivo samples). RESULTS: For both in vitro and ex vivo samples, notable differences between APTT reagents with respect to heparin sensitivity were noted. This indicates that a uniform therapeutic range of 1.5-2.5 calculated by the APTT ratio may not be appropriate for all reagents. Reagent sensitivity in ex vivo samples was substantially different to that in in vitro samples. CONCLUSIONS: The results of this large series of laboratories clearly indicate that reagent specific therapeutic ranges may be necessary, and that samples prepared by the addition of heparin to normal plasma in vitro can be misleading and should not be used.

Acute Disease↗

Improvement of the MALDI-TOF analysis of DNA with thin-layer matrix preparation.

A new method of sample preparation was developed for MALDI-TOF-MS analysis of oligonucleotides. First, aqueous DNA samples are dispensed and allowed to dry. Then 6-aza-2-thiothymine matrix dissolved in nonaqueous volatile solvents is applied on top of the DNA residue to form a thin homogeneous film. MALDI-TOF analysis shows such preparation generates much better shot-to-shot and sample-to-sample reproducibility and essentially eliminates the need to search for "hot" spots. The increased homogeneity of the matrix/analyte crystal distribution results in significant improvement for quantitative and high-throughput analyses of DNA. Using this method, isotopically resolved oligonucleotide spectra up to a 24-mer can also be easily obtained in a reflectron instrument. Due to the ease of preparation, this method could be widely useful for a number of applications such as for assays that are performed on surface in vitro, as the thin-layer matrix could be applied directly for MALDI analysis.

DNA↗

Colorimetric one-tube nested PCR for detection of Trichomonas vaginalis in vaginal discharge.

A colorimetric one-tube nested PCR was developed for the detection of Trichomonas vaginalis in clinical vaginal discharge specimens. A family of 650-bp specific DNA repeats from the T. vaginalis genome was targeted. There was no cross-reaction with human DNA or other infectious agents, including Pentatrichomonas hominis and Giardia lamblia. The colorimetric assay was applied as an adjunct to nested PCR for semiquantitative determination of T. vaginalis DNA at levels corresponding to 1 to 1,000 parasites. PCR of samples prepared by a rapid boiling method was as sensitive and specific as PCR of samples prepared by the standard DNA extraction method: the equivalent of one T. vaginalis organism in 20 microliters of vaginal discharge could be detected. The colorimetric nested PCR was compared with wet mount and culture for the detection of T. vaginalis. A total of 378 clinical vaginal discharge specimens from symptomatic patients were examined; 31 patients were positive for T. vaginalis both by culture and by nested PCR. However, only 17 of these 31 patients were positive by wet mount examination. In addition, of 113 asymptomatic patients, 9 were positive for T. vaginalis by nested PCR. Of these nine PCR-positive patients, only two were also positive both by wet mount and by culture, four patients were positive by culture but negative by wet mount, and three patients were negative both by wet mount and by culture. No specimens negative by nested PCR were positive by wet mount or by culture. The three asymptomatic patients with PCR-positive but wet mount- and culture-negative samples were subsequently found to have T. vaginalis infection after repeated and prolonged culture was performed. This colorimetric nested PCR was very sensitive compared with culture for the diagnosis of vaginal trichomoniasis, especially asymptomatic T. vaginalis infection. It is also simple, specific, rapid, and semiquantitative.

Animals↗

Comparison of sample fixation and the use of LDS-751 or anti-CD45 for leukocyte identification in mouse whole blood for flow cytometry.

Flow cytometry methods used to measure leukocyte function often entail sample preparation procedures that cause artifactual cell activation. To avoid leukocyte activation by isolation techniques, some preparation methods use fluorescent markers to discriminate leukocytes from erythrocytes in whole blood. One of these markers, laser dye styryl-751(LDS-751), has been used to distinguish leukocytes by staining nucleic acid, but has been found to stain other blood cells and dead cells indiscriminately. Thus, LDS-751 may not be an appropriate reagent for leukocyte identification in whole blood. Fixing samples with formaldehydes increases cell permeability and causes surface protein cross-linking that may alter staining of both intra- and extracellular markers. The degree of this sample alteration by formaldehyde fixation, however, remains in question. In addition, little is known about flow cytometry and sample preparation methods in mouse whole blood. The purpose of this study was to determine if labeling leukocytes with a monoclonal antibody specific to leukocyte common antigen (CD45) was superior to labeling with LDS-751 and to determine the effect of sample fixation on a mouse whole blood preparation for flow cytometry. Samples were incubated with CD16/CD32 Fc receptor blocker, and either 10 microg/ml LDS-751 or phosphate buffered saline (PBS). The samples were then fixed with paraformaldehyde or diluted with PBS followed by incubation with 5 microg/ml PerCP-conjugated anti-CD45, 5 microg/ml FITC-conjugated anti-CD11b, or 80 microM dichlorofluorescein diacetate. We found that samples labeled with LDS-751 demonstrated decreased fluorescence intensity for granulocyte CD11b expression and ROS production compared to samples labeled with anti-CD45. In addition, sample fixation decreased mean fluorescence intensity in samples labeled with either LDS-751 or anti-CD45. We conclude that labeling leukocytes with monoclonal antibody CD45 in a mouse whole blood preparation is preferable, as it provides improved measurement of leukocyte indices compared to LDS-751. Also, while sample fixation prior to antibody staining caused a decrease in overall fluorescence; it can be used to successfully identify extra-cellular markers.

Animals↗

Accurate nucleic acid concentrations by nuclear magnetic resonance.

Determination of the concentration of biochemical samples often yields values with uncertainties of 10-20% or more. This paper details a protocol for use with 500- to 600-MHz NMR spectrometers to measure approximately 1mM concentrations within +/-1-3% accuracy. With suitable precautions, all compounds have equal NMR "absorption coefficients" for protons. About 2mg of sample are needed for proteins and nucleic acids with MW=5000, although less accurate determinations could be made with smaller amounts. The technique utilizes standardized internal reference reagent compounds, cacodylic acid or 3-(trimethylsilyl)propionic-2,2,3,3-d(4) acid sodium salt. Spectra were signal-averaged using long interpulse delays so that integrals of nonexchangeable protons could be quantified relative to the reference standard. Accurate determinations require careful optimization of the homogeneity of the magnetic field and meticulous attention to sample preparation and spectral processing. The main source of error is usually the accuracy of micropipets. If sample preparation errors could be eliminated, the lower limit of accuracy with the current generation of NMR spectrometers is probably near 0.4%. However, this would require >99.5% sample purity. Methods are described to establish the concentration of the standards, and applications are illustrated with DNA mono- and oligonucleotides. Similar procedures should apply to proteins, polysaccharides, and other biomolecules, with about the same accuracy and precision.

Cacodylic Acid↗

[Detection of the annatto dye norbixin/bixin in cheese using derivative spectroscopy and high performance liquid chromatography (HPLC)].

A derivative spectroscopic method and a HPLC-method are described for the determination of the annatto dye-stuffs, norbixin and bixin, in cheese. Both methods enable a simple and quick sample preparation since the separation of beta-carotene and fat is not required. The sample preparation step consists of extraction with acetone, filtration, evaporation of the extract and separation of water residues by the addition of a few milliliters of absolute ethanol. This is followed by evaporation and extraction of the residual solution with chloroform/acetic acid (99.5 +/- 0.5) for the derivative spectroscopic method or with acetone for the HPLC method. The qualitative detection (detection limit greater than 0.67 mg/kg, depending on the genuine beta-carotene content) as well as the quantitative determination is possible by means of the derivative spectroscopic method. Therefore, this technique may be used within the rigorous Austrian regulations or for controlling the quantities and limits of annatto dye-stuffs in cheese, if its application is allowed. The method also has the advantage of quick detection (only 75 s) and saving of material used. The HPLC method allows for the separation and quantification of norbixin and bixin as well as the other carotenoids such as beta-carotene, beta-apo-8'-carotenal and beta-apo-8'-carotenoic acid--ethylester, which may also be found in varieties of cheese (detection limit of norbixin and bixin: 0.2 mg/kg). The time required for the separation of the above mentioned substances is 20 min and the HPLC method is proposed for the confirmation of low concentrations of these substances.

Bixaceae↗

EXAFS study of U(VI) uptake by calcium silicate hydrates.

Among the different cement minerals, calcium silicate hydrates (C-S-H) are the prime candidates for heavy metal binding because of their abundance and appropriate structure. Immobilization processes of heavy metals by cementitious materials, and in particular C-S-H phases, thus play an important role in multibarrier concepts developed worldwide for the safe disposal of hazardous and radioactive wastes. In this study, the uptake of U(VI) by C-S-H has been investigated using X-ray absorption fine structure (XAFS) spectroscopy. C-S-H phases were synthesized using two different procedures: One is based on the mixing of CaO and SiO2 solids ("direct reaction" method); for the other one starting solutions of Ca and Si are used ("solution reaction" method). XAFS investigations were carried out on samples doped with U(VI). U(VI) was either sorbed onto previously precipitated C-S-H phases (sorption samples) or added during C-S-H synthesis (coprecipitation samples). The coordination environment of U(VI) in the sorption samples was found to be independent of the procedure used for C-S-H synthesis. A split equatorial oxygen shell (Oeq1: R=2.23-2.27 A; Oeq2: R=2.36-2.45 A), neighboring silicon atoms at short (R=3.07-3.11 A) and long (R=3.71-3.77 A) distances, and neighboring Ca atoms (R=3.77-3.81 and 4.15-4.29 A) were observed for all the samples. The structural parameters resemble those reported for uranophane. The coordination environment of U(VI) in the coprecipitation samples depends on the method used for C-S-H synthesis, and further, the spectra differ from those determined for the sorption samples. UU backscattering contributions were observed in the samples prepared using the direct reaction method, whereas no split equatorial shell appeared in the samples prepared using the solution reaction method.

Absorptiometry, Photon↗

Fast automated extraction and clean-up of biological fluids for polychlorinated dibenzo-p-dioxins, dibenzofurans and coplanar polychlorinated biphenyls analysis.

A fast automated extraction and clean-up procedure for low-level analysis of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and coplanar polychlorinated biphenyls (cPCBs) in biological fluids is presented. Online extraction of prepared fluids is carried out using disposable octadecyl bonded (C(18)) solid-phase extraction columns. Extracts are then cleaned up through disposable multi-layer silica (acidic, basic and neutral) and dispersed PX-21 carbon columns. This new methodology is compared with classical Soxhlet extraction and manual solid-phase extraction in terms of repeatability, reproducibility, accuracy and recovery rates for reference and certified materials. Robustness is evaluated on different matrices, such as cow's milk, breast milk and human serum. As a consequence of the reduced number of reusable glassware used, as well as lowering of solvent consumption, recorded blank levels are decreased in favor of limits of detection (LODs). Total analysis time and cost are further reduced using simultaneous sample preparation units and the sample throughput is increased compared to classical methods. As a result, this new approach appears to be suitable for the fast sample preparation often required for such fluids in case of emergency foodstuffs analysis or during large epidemiological studies.

Animals↗

Application of comprehensive two-dimensional gas chromatography for the assessment of oil contaminated soils.

A crucial step in the remediation of oil contaminated soils is the characterization of the pollution. Information on the chemical composition is used to assess the toxicity (and thus the need for remediation) and to determine the most appropriate technology for treatment. Mostly these analyses are carried out in routine environmental laboratories using gas chromatography with flame ionization detection (GC/FID) based on a protocol developed by the Total Petroleum Hydrocarbon Criteria Working Group (TPHCWG). In the present study, an alternative method was developed using comprehensive two-dimensional gas chromatography (GCXGC) with FID. Sample preparation was limited to pressurized liquid extraction (PLE), and the analysis was carried out on a commercially available instrument with a conventional column combination (RTX-1/BPX50) and with standard chromatographic software. Compared to the TPH method, the group-types in the GCXGC analysis are chemically better defined and more specific information is obtained especially for the (toxicologically important) aromatic hydrocarbon fraction. Preliminary results indicate that higher recoveries and lower RSDs are obtained with GCXGC, probably because of the less complex sample preparation. Furthermore a data processing method was developed to generate TPH results from GCXGC data; the volatility distribution profiles compared very well with conventional TPH data. The possibility of extracting physicochemical properties directly from the GCXGC chromatogram was briefly explored, but software limitations hindered this promising application.

Analytic Sample Preparation Methods↗

Preparation of cross-sectional transmission electron microscopy samples by electron beam lithography and reactive ion etching.

A cross-sectional sample preparation technique is described that relies on lithographic and dry-etching processing, thus avoiding metallographic polishing and ion milling. The method is capable of producing cross-sectional transmission electron microscopy samples with a large amount of transparent area (1 micron x 2.5 mm) which allows the examination of many patterned test sites on the same sample from the same chip of a silicon wafer. An example of the application of the technique is given for localized oxidation through a mask.

Microscopy, Electron↗

Direct real-time PCR quantification of Campylobacter jejuni in chicken fecal and cecal samples by integrated cell concentration and DNA purification.

Campylobacter jejuni is a major cause of diarrheal disease and food-borne gastroenteritis. The main reservoir of C. jejuni in poultry is the cecum, with an estimated content of 6 to 8 log10 CFU/g. If a flock is infected with C. jejuni, the majority of the birds in that flock will harbor the bacterium. Diagnostics at the flock level could thus be an important control point. The aim of the work presented here was to develop a complete quantitative PCR-based detection assay for C. jejuni obtained directly from cecal contents and fecal samples. We applied an approach in which the same paramagnetic beads were used both for cell isolation and for DNA purification. This integrated approach enabled both fully automated and quantitative sample preparation and a DNA extraction method. We developed a complete quantitative diagnostic assay through the combination of the sample preparation approach and real-time 5'-nuclease PCR. The assay was evaluated both by spiking the samples with C. jejuni and through the detection of C. jejuni in naturally colonized chickens. Detection limits between 2 and 25 CFU per PCR and a quantitative range of >4 log10 were obtained for spiked fecal and cecal samples. Thirty-one different poultry flocks were screened for naturally colonized chickens. A total of 262 (204 fecal and 58 cecal) samples were analyzed. Nineteen of the flocks were Campylobacter positive, whereas 12 were negative. Two of the flocks contained Campylobacter species other than C. jejuni. There was a large difference in the C. jejuni content, ranging from 4 to 8 log10 CFU/g of fecal or cecal material, for the different flocks tested. Some issues that have not yet promoted much attention are the prequantitative differences in the ability of C. jejuni to colonize poultry and the importance of these differences for causing human disease through food contamination. Understanding the colonization kinetics in poultry is therefore of great importance for controlling human infections by this bacterium.

Animals↗

Platinum determination by inductively coupled plasma-sector field mass spectrometry (ICP-SFMS) in different matrices relevant to human biomonitoring.

The analytical challenges of Pt determination by ICP-SFMS posed by different human tissues and fluids have been critically assessed. Investigated samples were (1) urine, (2) serum of cancer patients sampled during chemotherapy with carboplatin, (3) microdialysates (20 micro L sample volume) collected from tumor and non-tumor tissue, and, finally-for the first time-(4) human lung tissue to study background concentrations of inhaled platinum. Sample preparation involved microwave digestion and open vessel treatment or simple dilution (microdialysates). Depending on the sample preparation and introduction systems used (microconcentric nebulization, ultrasonic nebulization with and without membrane desolvation) excellent procedural detection limits (3s criterion) of 0.35 pg g(-1) for urine, 420 pg g(-1) for serum, 400 pg g(-1) for lung tissue and 13 pg g(-1) for microdialysates could be obtained. Ultratrace concentrations of 1-40 pg g(-1), and 1000-3000 pg g(-1) were measured in urine and human lung tissue, respectively, as typical for samples in environmental studies. Quantification was carried out by IDMS and standard addition in the case of urine samples. Internal standardization could not correct for non-spectral interferences in external calibration. In the serum and microdialysates of patients during chemotherapy with carboplatin, elevated Pt levels ranging between 0.01 and 10 micro g g(-1) were determined by external calibration ((195)Pt isotope). For all investigated samples spectral interferences could be excluded by following different strategies. High-resolution control measurements ((194)Pt, (195)Pt) were performed in the case of elevated Pt levels, i.e. for microdialysates and serum samples. An Hf/Pt ratio of 0.4 was determined in human lung samples. An HfO formation ratio of 0.2% was assessed for standard solutions at the present experimental conditions, revealing that the contribution of (179)Hf(16)O, (178)Hf(17)O, (177)Hf(18)O to the (195)Pt isotope signal used for quantification was not significant.

Blood Chemical Analysis↗

Direct injection versus liquid-liquid extraction for plasma sample analysis by high performance liquid chromatography with tandem mass spectrometry.

Direct injection versus liquid-liquid extraction for post-dose human plasma sample analysis by high performance liquid chromatography with tandem mass spectrometry (LC/MS/MS) have been studied using a drug candidate compound. For the direct-injection method, an Oasis(R) HLB column (1 x 50 mm, 30 micrometer) was used as the on-line extraction column and a conventional Waters symmetry C18 column (3.9 x 50 mm, 5 micrometer) was used as the analytical column. Each plasma sample (100 microL) was mixed with 100 microL of a working solution of the internal standard in aqueous 0.05 M ammonium acetate (pH 6.9), and portions (10 microL) of these samples were then injected into the LC/MS/MS system. For the liquid-liquid extraction method, a YMC Basic C18 column (2.0 x 50 mm, 5 micrometer) was used as the analytical column. Each sample (0.5 mL) was extracted with methyl tert-butyl ether and the extract was reconstituted and injected into the LC/MS/MS system. The total analysis time for both methods was 2.0 min per sample. The accuracy, inter-day precision and intra-day precision obtained from the quality control samples were within 8% for both methods. The analysis results of post-dose human plasma samples showed that the deviations of 91% of the concentrations obtained using the direct-injection method were within +/-20% from the concentrations obtained using the liquid-liquid extraction method, and the overall average percentage deviation was -1.5%. The results showed that the two methods were equivalent in terms of total chromatographic run time, accuracy and precision. However, for a batch of 100 samples, the sample preparation time for the direct-injection method was only about 25% of the time required for liquid-liquid extraction. This decrease in sample preparation time resulted in the doubling of the overall sample analysis throughput.

Chromatography, High Pressure Liquid↗

Analytical reproducibility in (1)H NMR-based metabonomic urinalysis.

Metabonomic analysis of biofluids and tissues utilizing high-resolution NMR spectroscopy and chemometric techniques has proven valuable in characterizing the biochemical response to toxicity for many xenobiotics. To assess the analytical reproducibility of metabonomic protocols, sample preparation and NMR data acquisition were performed at two sites (one using a 500 MHz and the other using a 600 MHz system) using two identical (split) sets of urine samples from an 8-day acute study of hydrazine toxicity in the rat. Despite the difference in spectrometer operating frequency, both datasets were extremely similar when analyzed using principal components analysis (PCA) and gave near-identical descriptions of the metabolic responses to hydrazine treatment. The main consistent difference between the datasets was related to the efficiency of water resonance suppression in the spectra. In a 4-PC model of both datasets combined, describing all systematic dose- and time-related variation (88% of the total variation), differences between the two datasets accounted for only 3% of the total modeled variance compared to ca. 15% for normal physiological (pre-dose) variation. Furthermore, <3% of spectra displayed distinct inter-site differences, and these were clearly identified as outliers in their respective dose-group PCA models. No samples produced clear outliers in both datasets, suggesting that the outliers observed did not reflect an unusual sample composition, but rather sporadic differences in sample preparation leading to, for example, very dilute samples. Estimations of the relative concentrations of citrate, hippurate, and taurine were in >95% correlation (r(2)) between sites, with an analytical error comparable to normal physiological variation in concentration (4-8%). The excellent analytical reproducibility and robustness of metabonomic techniques demonstrated here are highly competitive compared to the best proteomic analyses and are in significant contrast to genomic microarray platforms, both of which are complementary techniques for predictive and mechanistic toxicology. These results have implications for the quantitative interpretation of metabonomic data, and the establishment of quality control criteria for both regulatory agencies and for integrating data obtained at different sites.

Animals↗

Homogeneity check of agricultural and food industries samples using near infrared spectroscopy.

Samples distributed in proficiency testing schemes (PTS) need to be homogeneous in order to be sure that if a laboratory has a result different from the other laboratories, its error can be attributed to its analysis method and not to its sample. This control must be done according to the ISO 13528 draft standard before sending the samples to the laboratories. It can be done by determining homogeneity targets by sub-contracting to accredited laboratories using reference methods, but this engenders logistic and financial problems. That is why a homogeneity check using Near Infrared Spectroscopy (NIR) has been developed for agricultural and food industries samples prepared for PTS at Bipea (Bureau Interprofessionnel d'Etudes Analytiques). To evaluate the homogeneity among samples, this procedure involves a comparison of NIR spectra, the determination of global homogeneity criteria and the use of control charts. The method of control developed and carried out at Bipea allows the rapid and easy monitoring of the performance of the sample preparation.

Crops, Agricultural↗

Development of silicon microstructures and thin-film MALDI target plates for automated proteomics sample identifications.

Here we report on the development of a proteomic platform utilizing a piezoelectric flow-through dispensing unit made from silicon microstructures. The use of a novel surface coating, where matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI MS) targets were uniformly precoated with a thin film of matrix/nitrocellulose, made the sample preparation straightforward and enabled the enrichment and analysis of proteins at low levels in proteomics samples. We demonstrate this by analyzing excised spots in a biological sample originating from a human fetal fibroblast cell line that was subjected to 2D gel-electrophoresis. Furthermore, a sample deposition rate below 30 Hz results in an increased analyte density on the dispensed sample spot, rendering signal amplification. In general, the sensitivity for proteins and peptides can be enhanced 10-50 times compared to traditional MALDI sample preparation techniques.

Animals↗

Influence of cultivar, maturity, and sampling on blackberry (Rubus L. Hybrids) anthocyanins, polyphenolics, and antioxidant properties.

Total anthocyanin pigments increased from 74.7 to 317 mg/100 g fresh weight (FW) from underripe to overripe for Marion blackberries and from 69.9 to 164 mg/100 g FW for Evergreen blackberries. Total phenolics did not show a marked change with maturity with values slightly decreasing from underripe to ripe. Antioxidant activities, while increasing with ripening, also did not show the marked change that total anthocyanins exhibited. The impact of variation due to plots, subsampling, sample preparation, and measurement on Marion composition was examined in detail. Plot-to-plot and sample differences were the major contributors to variation, with sample preparation being an important contributor for some parameters. Measurement variation was a relatively small component of the total variation. Total anthocyanins for 11 blackberry cultivars ranged from 131 to 256 mg/100 g FW (mean = 198), total phenolics ranged from 682 to 1056 mg GAE/100 g FW (mean = 900), oxygen radical absorbance capacity ranged from 37.6 to 75.5 micromol TE/g FW (mean = 50.2), and ferric reducing antioxidant power ranged from 63.5 to 91.5 micromol TE/g FW (mean = 77.5).

Anthocyanins↗

Electronic platelet counts with the Coulter counter. Reassessment of a correction factor.

Platelet counts are determined on the Coulter electronic counter by counting the diluted platelet-rich plasma obtained by sedimentation or centrifugation of whole blood. In calculating the whole-blood platelet count, an empirical correction factor for platelet-free plasma trapped by sedimented erythrocytes has been recommended, and a widely-distributed circular slide rule calculator incorporates the correction factor. In this study, visual and electronic platelet counts were compared in 100 specimens with counts ranging from 10 to 1,100 X 10(3) per mul and hematocrits ranging from 17.5 to 48.5%. Platelet-rich plasma samples prepared by a centrifugation method (Plateletfuge) gave machine counts in close agreement with those of samples prepared by sedimentation. Whole-blood platelet counts determined with the circular calculator were consistently lower than visual counts, with an average difference of -17%. The electronic counts were recalculated after elimination of the correction factor, and agreement then improved to an average difference of only +1.6%. The correction factor for trapped platelet-free plasma leads to erroneously low values and should not be used.

Blood Cell Count↗