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PubMed1992

Genomic DNA microextraction: a method to screen numerous samples.

Many experimental designs require the analysis of genomic DNA from a large number of samples. Although the polymerase chain reaction (PCR) can be used, the Southern blot is preferred for many assays because of its inherent reliability. The rapid acceptance of PCR, despite a significant rate of false positive/negative results, is partly due to the disadvantages of the sample preparation process for Southern blot analysis. We have devised a rapid protocol to extract high-molecular-weight genomic DNA from a large number of samples. It involves the use of a single 96-well tissue culture dish to carry out all the steps of the sample preparation. This, coupled with the use of a multichannel pipette, facilitates the simultaneous analysis of multiple samples. The procedure may be automated since no centrifugation, mixing, or transferring of the samples is necessary. The method has been used to screen embryonic stem cell clones for the presence of targeted mutations at the Hox-2.6 locus and to obtain data from human blood.

Animals↗
PubMed2000

Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues.

The changes in the ion signals in the isotope cluster, mass resolution, signal-to-noise ratio and mass accuracy for matrix-assisted laser desorption/ionization (MALDI) of DNA oligonucleotides (dGGATC, dCAGCt, and dAACCGTT) and their fragment ions were evaluated, and these data were compared with those obtained using 3-hydroxypicolinic acid. Mass spectra obtained by using 2,5-dihydroxybenzoic acid (2,5-DHB) appear to have differences from the theoretical isotopic clusters, which arise by reductive hydrogenation producing a second peak at the M + 2 isotope of the native oligonucleotide. Based on the patterns of the isotopic envelope observed in the in-source decay fragments, we propose that cytosine is the site of reduction. We do not find evidence of reduction of oligonucleotides, viz. dTGGGGTT, that do not contain cytosine; however, 2'-deoxycytidine and 2'-deoxycytidine-5'-monophosphate undergo reductive hydrogenation. Several experiments were carried out in an effort to determine whether the reductive hydrogenation occurs during sample preparation or as a result of laser irradiation. The results of these experiments suggest that it occurs during sample preparation. The relative intensities of ion signals corresponding to the reduced base can be altered by using different matrix additives (aminonaphthalenes) or a different substrate (copper). Also, the oxidized form of 2,5-DHB is trapped by reaction with the side chain of cysteine in glutathione, providing evidence that the reaction occurs in solution as the matrix crystallizes.

Base Sequence↗
PubMed2005

Gas chromatographic method for the analysis of allelopathic natural products in rye (Secale cereale L.).

Accurate and reproducible methods for the analysis of plant allelochemicals are a requirement for the study of chemical interactions between plants. This paper describes a method for sample preparation and quantitative analysis of the allelopathic chemical content of rye (Secale cereale L.) using gas chromatography (GC). Sample preparation consists of extraction of freeze-dried rye vegetative tissue with aqueous ethanol followed by partitioning of the allelochemicals into ethyl acetate, evaporation, and derivatization using the trimethylsilylating reagent N-methyl-N-trimethylsilyltrifluoroacetamide. GC analysis of the silylated mixture was performed using flame ionization detection. This method permits analysis of all known rye allelopathic agents including 2,4-dihydroxy-1,4-benzoxazin-3-one, its corresponding glucoside, 2-benzoxazolinone, beta-hydroxybutyric acid, and beta-phenyllactic acid. Identities of all compounds were confirmed by GC/MS analysis.

3-Hydroxybutyric Acid↗
PubMed2006

Ion-pair solid-phase extraction and gas chromatography-mass spectrometric determination of acidic hydrolysis products of chemical warfare agents from aqueous samples.

The chemical warfare agents (CWA) degrade rapidly in aqueous samples and convert to acidic degradation products. Extraction and identification of the degradation products from complex matrices using simple sample preparation and sensitive detection and identification is the most important step in the off-site analysis of samples. In this present study, we report a simple sample preparation step based on ion-pair (IP) solid-phase extraction (SPE) for the extraction of acidic degradation products of CWA namely methyl, ethyl, propyl phosphonic acids, thiodiglycolic acid and benzilic acid. The analysis was performed on GC-MS in electron impact ionization mode. Three IP reagents triethylamine (TEA), tetrabutylammonium bromide (TBAB) and cetyltrimethyl ammonium bromide (CTAB) were used. The recoveries were estimated using the internal and external standard methods. The recovery of the compounds was almost negligible when TEA was used as IP reagent. The recoveries obtained when TBAB and CTAB were used as IP reagents were high and reproducible. The recovery of test chemicals is above 90%, except for methyl phosphonic acid and ethylphosphonic acid (20.6 +/- 3.2% and 35.8 +/- 2.5%, respectively). The minimum detection limits of the method were calculated for all chemicals in both full scan and selected ion monitoring modes. The test chemicals could be detected in microgram per litre quantities by the IP-SPE method.

Cetrimonium↗
PubMed2002

Evaluation of human thymus and activation-regulated chemokine concentrations in blood using a new sandwich ELISA based on monoclonal antibodies.

BACKGROUND: CC chemokine TARC (thymus and activation-regulated chemokine), a potent chemoattractant for Th2 lymphocytes, is thought to play important roles in inflammatory diseases. We developed a new sensitive enzyme-linked immunoassay (ELISA) for human TARC (hTARC) to accurately measure and evaluate its concentrations in blood. METHODS: An ELISA was developed using two established monoclonal antibodies against hTARC. Using this assay, we observed changes of hTARC concentrations in serum and plasma obtained from individual subjects. Improvements to the assay were made to allow use for the clinical evaluation of samples from atopic dermatitis (AD). RESULTS: The lower detection limit of the ELISA was 1.4 pg/ml for a 25 microl sample volume. Other assay characteristics were enough to satisfactorily measure hTARC in biological fluids. This ELISA revealed that changes in serum and plasma concentrations were related to sample handling before separation from blood. With appropriate sample preparation, significant increases of hTARC were observed in patients with AD in comparison with normal subjects. CONCLUSIONS: Appropriate sample preparation is important for clinical studies on hTARC. Accurate measurement using our ELISA method offers a suitable clinical index for evaluating the severity of allergic diseases of Th2-dominant disorders, such as AD.

Antibodies, Monoclonal↗
PubMed1997

Determination of the lactone and lactone plus carboxylate forms of 9-aminocamptothecin in human plasma by sensitive high-performance liquid chromatography with fluorescence detection.

Two sensitive reversed-phase high-performance liquid chromatographic fluorescence methods, with simple sample handling at the site of the patient, are described for the determination of the lactone and lactone plus carboxylate forms of 9-aminocamptothecin (9AC). For 9AC lactone, the sample preparation was a liquid-liquid extraction with acetonitrile-n-butyl chloride (1:4, v/v), whereas the sample preparation for 9AC total (lactone plus carboxylate) was a simple deproteinization with 5% perchloric acid-methanol (1:1, v/v), which results in the conversion of the carboxylate into the lactone form. The lower limits of quantitation were 50 pg/ml and 100 pg/ml for 9AC lactone and 9AC total, respectively. The within-run precisions at four tested concentrations were < or = 6.3% for 9AC lactone and < or = 5.3% for 9AC total. The between-run precisions were < or = 8.9% and < or = 5.6%, respectively. The assays were developed to enable pharmacological analysis of 9AC in a bioavailability and oral phase I study in patients with solid tumors.

Antineoplastic Agents↗
PubMed1997

Use of binary solvent systems in the MALDI-TOF analysis of poly(methyl methacrylate).

Two of the main problems associated with matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) analysis of polymers are mass discrimination and poor reproducibility. This paper shows that the use of binary solvent systems is one of the causes of these problems. It was observed that the presence of a second solvent such as water in the PMMA solution could cause significant mass discrimination and varying polymer distributions, which can be varied by over 50% when PMMA 4K was used as the polymer sample. In general, a small amount of a second solvent tends to result in less severe mass discrimination but varying distributions, while large amounts of a second solvent are more likely to cause more systematic and severe mass discrimination. Except for a few cases, mass discrimination was observed to be against larger oligomers. Moreover, it was observed that this effect varies with the matrix, main solvent, and sample preparation used. The importance of this work is that it provides guidance for one to develop a better sample preparation protocol to minimize the mass discrimination and poor reproducibility problems. Several potential sources leading to water contamination were identified. Finally, a simple method to verify if amounts of a second solvent are sufficiently high to cause mass discrimination is also discussed.

Furans↗
PubMed2002

Sampling wheat for deoxynivalenol.

The variability associated with testing wheat for deoxynivalenol (DON) was measured using a 0.454 kg sample, a Romer mill, 25 g of comminuted subsample and the Romer Fluoroquant analytical method. The total variability was partitioned into sampling, sample preparation, and analytical variability components. Each variance component was found to be a function of the DON concentration and equations were developed to predict each variance component using regression techniques. The effects of sample size, subsample size, and number of aliquots on reducing the variability of the DON test procedure were also determined. Using the test procedure described above, the coefficient of variation (CV) associated with testing wheat at 5 ppm DON was found to be 13.4%. The CVs associated with sampling, sample preparation, and analysis were 6.3, 10.0, and 6.3%, respectively. The sample variations associated with testing wheat are relatively small when compared to CVs associated with testing other commodities for other mycotoxins such as aflatoxin in peanuts. Even with the use of a small sample size (0.454 kg), the sampling variation was not the largest source of error as found in other mycotoxin test procedures.

Algorithms↗
PubMed1986

Application of robotics in blood banking.

To demonstrate the feasibility of using robots in blood banking applications several prototype systems were developed. Activities associated with sample testing and component preparation were examined. In one project, a general-purpose laboratory robot (Zymate Laboratory Automation System, Zymark, Inc., Hopkinton, Mass.) was configured to prepare samples for microplate-based ABO/Rh testing. In a second project, this same robot was configured to carry out specific steps in evaluating bar-coded labels, as part of a quality control procedure. A fluid-handling robot (Sampler 505, Tecan AG, Hombrechtikon, Switzerland) was used to prepare the dilution of serum samples for the evaluation of an anti-HTLV-III test kit. It was then configured to aspirate, dilute and dispense samples for anti-HTLV-III and HBsAg testing. This robotic system is now in field trial. The use of large industrial robots for automating component production was also considered. The key element in this design was the development of a fixture that would hold the blood bag set during the balancing, centrifugation and expressing steps. However, a fixture which was capable of performing these operations and that was equivalent in size and adaptable to a standard centrifuge bucket could not be fabricated.

Antibodies, Viral↗
PubMed2005

Dispersive solid-phase extraction for the determination of sulfonamides in chicken muscle by liquid chromatography.

A new, fast and low-cost sample preparation for the determination of sulfonamide (SA) residues in chicken muscle by LC technique has been developed. The procedure involves single extraction of sample with acetonitrile, followed by a rapid clean-up and was called "dispersive solid-phase extraction" (dispersive SPE). Using dispersive SPE 25 mg of octadecyl sorbent was added to 1 ml of acetonitrile extract, mixed and centrifuged. The acetonitrile layer was evaporated and residue was dissolved in acetate buffer (pH 3.5). Analysed compounds were detected by fluorescence detector after pre-column derivatization with fluorescamine. The separation of analytes was performed with gradient elution with mobile phase methanol: 2% acetic acid and RP-LC analytical column. The whole procedure was evaluated for six sulfonamides (sulfadiazine, sulfamerazine, sulfamethazine, sulfametoxypirydazine, sulfametoxazole and sulfadimetoxine) according to the European Commission Decision 2002/657/EC. Specificity, decision limit (CCalpha), detection capacity (CCbeta), trueness and precision were determined during validation process. The dispersive SPE with octadecyl sorbent was found suitable for sample preparation before sulfonamide determination in chicken muscle. As it was found the most of endogenous matrix components were removed and the analytes were isolated from spiked samples with recoveries above 90%. The used analytical conditions allow to successively separate all the tested sulfonamides with the limit of detection at the level of 1-5 microg/kg. The method is simple, rapid and more effective than conventional methods.

Animals↗
PubMed2000

Comparison of polyvinyl alcohol fixative with three less hazardous fixatives for detection and identification of intestinal parasites.

Polyvinyl alcohol (PVA) containing the fixative mercuric chloride is considered the "gold standard" for the fixation of ova and parasites in the preparation of permanently stained smears of stool specimens. However, mercuric chloride is potentially hazardous to laboratory personnel and presents disposal problems. We compared three new alternative, nontoxic fixatives with PVA, analyzing ease of sample preparation and quality of smears. Sixty-eight fresh stool specimens were divided into aliquots and placed in each of four different fixatives: PARASAFE (PS) (Scientific Devices Laboratory, Inc., Des Plaines, Ill.), ECOFIX (EC) (Meridian Diagnostics, Inc., Cincinnati, Ohio), Proto-Fix (PF) (Alpha-Tec Systems, Inc., Vancouver, Wash.), and low-viscosity PVA fixative (PVA) (Meridian). Specimens were processed and stained according to each manufacturer's directions. Parasites were found in 31 of 68 slide preparations with PVA, 31 with PF, 30 with EC, and 30 with PS. Blastocystis hominis and Iodamoeba bütschlii were preserved in a readily identifiable state by all methods of fixation. However, some parasites were more easily identified with some of the fixatives because of differences in parasite distortion. For example, Entamoeba histolytica (Entamoeba dispar) was detected in 13 stools fixed with PF, 7 with PVA, and 6 with EC but none with PS. Likewise, Chilomastix mesnili was identified in 13 specimens fixed with PF, 8 with EC, and 5 with PVA but only 1 with PS, while Entamoeba coli was seen much less frequently with PS than with the other three fixatives. A dirty background was observed in 41% of specimens prepared with PS, whereas background quality was acceptable with other fixatives. Sample preparation was most rapid with PS, although the EC method involved the fewest steps. In conclusion, PVA and PF produced the least parasite distortion, while PS proved unsatisfactory for the identification of E. histolytica, E. coli, and C. mesnili. Both PF and EC appear to be acceptable, environmentally safe substitutes for PVA.

Animals↗
PubMed2004

Drug release from alpha,beta-poly(N-2-hydroxyethyl)-DL-aspartamide-based microparticles.

Spherical pH-sensitive microparticles have been prepared by reverse phase suspension polymerization technique. Starting polymer has been alpha,beta-poly(N-2-hydroxyethyl)-DL-aspartamide (PHEA) partially derivatized with glycidylmethacrylate (GMA). PHEA-GMA copolymer (PHG) has been crosslinked in the presence of acrylic acid (AA) or methacrylic acid (MA) at various concentration. The obtained microparticles have been characterized by FT-IR spectrophotometry, particle size distribution analysis and scanning electron microscopy. In order to have information about water affinity of the prepared samples, swelling measurements have been carried out in aqueous media which simulate some biological fluids. The possibility to employ the prepared samples as pH-sensitive microparticles has been investigated by performing in vitro release studies. Experimental data have showed that the release rate from these microparticles depends on the environmental pH and the chemical structure of the drug.

Absorption↗
PubMed2005

DNA index, genome size, and electronic nuclear volume of vertebrates from the Miami Metro Zoo.

BACKGROUND: Flow cytometry is a rapid and reliable method for measuring nuclear DNA content and genome size. Fluorochrome binding characteristics, sample preparation and differences in DNA condensation, and availability of binding sites can cause variations in results obtained. METHODS: Blood samples from 82 vertebrate species were collected in 10% dimethyl sulfoxide and stained with propidium iodide/hypotonic citrate or 4,6-diamidino-2-phenylindole dihydrochloride for analysis of DNA content and electronic nuclear volume (ENV). Trout red blood cells (TRBCs), human peripheral blood lymphocytes, and human buccal cavity cells were used as internal standards. RESULTS: Mean fluorescence channel (MFC) values of TRBC and buccal cavity cells used as internal standards were stable at 15 to 120 min of propidium iodide staining. TRBCs mixed with other cells especially human peripheral blood cells showed an increase in MFC. ENV and MCF values were less variable in different species of birds than in reptiles or mammals. Genome size based on use of buccal cavity cells as the internal standard showed a high degree of correlation with previous reports. CONCLUSIONS: Proper selection and use of internal standards and sample preparation are essential for reliable determination of DNA content and genome size in vertebrates by flow cytometry.

Animals↗
PubMed2005

Conformational order of n-alkyl modified silica gels as evaluated by Fourier transform infrared spectroscopy.

The conformational behaviour of non-deuterated and selectively deuterated alkyl modified silica gels in the dry state is examined by variable temperature FT IR spectroscopy. In the present study, three systems are considered, which are distinguished by the length of the tethered alkyl chains (C9Hl9-, C18H37-, C22H45-). The desired information is obtained by the analysis of various conformational-sensitive IR bands, including CH2 wagging, CD2 stretching and CD2 rocking bands. The analysis of the CH2 wagging bands provides the relative amounts (i.e., integral numbers over the whole chain) of the kink/gauche-trans-gauche, double-gauche and end-gauche conformers in the tethered alkyl chains. From the analysis of the CD2 stretching and CD2 rocking bands information about the conformational order at a specific deuterated methylene segment is available. Here, the CD2 rocking band data are used to determine the amount of gauche conformers at the deuterated carbon positions C-4 and C-6, and C-12. It is found that the conformational order critically depends on the actual alkyl chain length, chain position and sample temperature. Particular emphasis is given to the impact of the external pressure during sample preparation on the alkyl chain conformations, about which so far no information is available. It is observed that the samples prepared as KBr pellets, which experienced a pressure of about 10 kbar, are characterised by a lower amount of gauche conformers. This substantial increase of conformational order is attributed to better alkyl chain packing along with a gain of intermolecular chain interactions.

Alkanes↗
PubMed1983

Alterations in dopaminergic function after subacute ethanol administration.

The in vivo and in vitro effects of d-amphetamine were assessed in rats after subacute (24 hr) administration of ethanol vapor (28 mg/l). Forty-eight hours after the termination of ethanol vapor inhalation, when the animals were tolerant to the hypothermic effect of ethanol, a decreased hypothermic response to d-amphetamine was detected, suggesting that functional changes in dopaminergic activity might be associated with ethanol tolerance. The hyperthermic effect of d-amphetamine was similar in the ethanol-tolerant and control animals. The d-amphetamine-stimulated release of [3H]dopamine from crude synaptosomal (P2) fractions of striatum was nearly abolished immediately after subacute ethanol administration. Samples prepared from ethanol-tolerant animals released less [3H]dopamine in response to d-amphetamine perfusion compared to samples prepared from control animals when tested 48 hr after ethanol vapor exposure. Subacute ethanol administration appears to produce long-acting changes in d-amphetamine-sensitive dopaminergic mechanisms.

Animals↗
PubMed2001

Application of inductively coupled plasma sector field mass spectrometry for elemental analysis of urine.

An analytical method using double focusing sector field inductively-coupled plasma mass spectrometry (sector field ICP-MS) for rapid simultaneous determination of 42 elements in urine is described. Sample preparation consisted of 20-fold dilution with 0.14 mol/l nitric acid in ultrapure water. The importance of controlling possible contamination sources at different sample preparation and analysis stages in order to achieve adequate method detection limits (DL) is emphasized. Correction for matrix effects was made using indium and lutetium as internal standards. Different approaches for accuracy assessment in urine analysis are evaluated. Additional information on trace element concentrations in a urine reference material is given. Between-batch precision was assessed from the analysis of separately prepared aliquots of the reference material and was better than 10% RSD for 32 of the elements. The robustness of the procedure was tested by analysis of about 250 samples in one analytical run lasting more than 50 hours. A statistical summary of results for 19 urine samples from non-exposed subjects is presented. For a majority of the elements tested concentrations were higher than the detection limit of the method.

Calibration↗
PubMed1998

Determination of organophosphorus pesticides in wheat flour by supercritical fluid extraction and gas chromatography with nitrogen-phosphorus detection.

Application of supercritical fluid extraction (SFE) for selective isolation of organophosphorus pesticides from a real-world matrix (wheat flour) has been described. The method uses extraction with supercritical carbon dioxide at 206.8 bar and 60 degrees C, followed by quantitation by gas chromatography with nitrogen-phosphorous detection without clean-up of the extracts. Comparison of SFE with a method currently employed for sample preparation (i.e., organic solvent extraction followed by liquid-liquid extraction and gel permeation chromatography clean-up) shows that the SFE technique simplifies the sample preparation step and speeds up the determination of organophosphorus pesticides in flour. Extraction times were 60 min for a 7 g sample size. This technique was able to determine organophosphorus pesticides (ethoprophos, diazinon, chlorpyrifos methyl, fenitrothion, parathion, phenthoate, EPN) in samples at the 10 ng/g level.

Chlorpyrifos↗
PubMed2000

Applications of solid-phase microextraction in food analysis.

Food analysis is important for the evaluation of the nutritional value and quality of fresh and processed products, and for monitoring food additives and other toxic contaminants. Sample preparation, such as extraction, concentration and isolation of analytes, greatly influences the reliable and accurate analysis of food. Solid-phase microextraction (SPME) is a new sample preparation technique using a fused-silica fiber that is coated on the outside with an appropriate stationary phase. Analyte in the sample is directly extracted to the fiber coating. The SPME technique can be used routinely in combination with gas chromatography (GC), GC-mass spectrometry (GC-MS), high-performance liquid chromatography (HPLC) or LC-MS. Furthermore, another SPME technique known as in-tube SPME has also been developed for combination with LC or LC-MS using an open tubular fused-silica capillary column as an SPME device instead of SPME fiber. These methods using SPME techniques save preparation time, solvent purchase and disposal costs, and can improve the detection limits. This review summarizes the SPME techniques for coupling with various analytical instruments and the applications of these techniques to food analysis.

Food Analysis↗