Automated, fluorescence-based approach for the specific diagnosis of chicken coccidiosis.

We have established a fluorescence-based electrophoretic approach for the specific identification of all seven currently recognised species of Eimeria infecting chickens. The second internal transcribed spacer (ITS-2) of ribosomal DNA is amplified by polymerase chain reaction (PCR) from any of the seven species using a single set of oligonucleotide primers (of which the reverse one is fluorescently labelled). The amplicons are heat-denatured, subjected to denaturing polyacrylamide gel electrophoresis in a 377 DNA sequencer (ABI). The chromatograms produced are stored electronically and then analysed using GeneScan 3.1 software. Using control DNA samples representing monospecific lines of Eimeria, regions in the chromatograms have been defined for the specific identification of each of the seven species, although some variation in the chromatograms (reflecting population variation) was detectable within two species. Electrophoretic reading and analysis is carried out automatically using a computer imaging system, thus making it a time- and cost-effective approach. It is well suited for high-throughput diagnostic screening of oocyst samples and should find applicability as a tool for prevalence studies, monitoring of coccidiosis outbreaks and the quality control of vaccines.     

High-resolution electrophoretic procedures for the identification of five Eimeria species from chickens, and detection of population variation

To overcome limitations of conventional approaches for the identification of Eimeria species of chickens, we have established high resolution electrophoretic procedures using genetic markers in ribosomal DNA. The first and second internal transcribed spacer (ITS-1 and ITS-2) regions of ribosomal DNA were amplified by polymerase chain reaction (PCR) from genomic DNA samples representing five species of Eimeria (E. acervulina, E. brunetti, E. maxima, E. necatrix and E. tenella), denatured and then subjected to denaturing polyacrylamide gel electrophoresis (D-PAGE) or single-strand conformation polymorphism (SSCP) analysis. Differences in D-PAGE profiles for both the ITS-1 and ITS-2 fragments (combined with an apparent lack of variation within individual species) enabled the unequivocal identification of the five species, and SSCP allowed the detection of population variation between some isolates representing E. acervulina, which remained undetected by D-PAGE. The establishment of these approaches has important implications for controlling the purity of laboratory lines of Eimeria, for diagnosis and for studying the epidemiology of coccidiosis.     

Solid-phase microextraction gas chromatography/mass spectrometry: a new method for species identification of truffles

This study describes a rapid method to identify different truffle species by analysis of their volatile compound fraction using static headspace solid-phase microextraction gas chromatography/mass spectrometry. The volatile organic compounds (VOCs) were extracted using a new 2-cm 50/30 microm DVB/CAR/PDMS fiber placed for 10 min in the headspace of the truffle sample with the vial maintained at 20 degrees C (in a thermostatically controlled analysis room). The mass spectra of the VOC chromatograms were represented as 'fingerprints' of the analysed samples. Next, stepwise factorial discriminant analysis afforded a limited number of characteristic fragment ions that allowed a classification of the truffle species studied. This new method provides an effective approach to rapid quality control and identification of truffle species by analysis of their volatile fraction. Moreover, this method offers the advantage of minimizing thermal, mechanical, and chemical modifications of the truffles, thereby reducing the risk of analytical artifacts.     

Fast identification of mycobacterium species by GC analysis with trimethylsulfonium hydroxide (TMSH) for transesterification

Trimethylsulfonium hydroxide (TMSH) reproducibly converts fatty acids bound in, e.g., biomolecules such as phospholipids and/or glycerides, into the corresponding fatty acid methyl esters (FAMEs). The transesterification can be performed at room temperature in a fast single step reaction. Surprisingly, secondary alcohols and mycolic acid cleavage products (MACPs) are also released from mycobacteria under these conditions. The complex reaction mixtures containing FAMEs, MACPs, and secondary alcohols can easily be separated by high resolution temperature-programmed capillary GC. Different species of mycobacteria give rise to characteristic chromatographic patterns and the amount of lipids from a single colony of mycobacteria is sufficient for reliable identification of the bacteria. The profiles of the chromatograms match well those obtained from other sample preparation techniques. The TMSH method of identification of mycobacteria from the patterns of the gas chromatograms is faster and more sensitive than conventional methods, which also involve transesterification. The identification of mycobacterial species by microbiological culture techniques is difficult to perform and requires several weeks.     

毛细管气相色谱法鉴定分析杆菌

本文利用ＯＶ－１０１熔融石英毛细管柱，对１５种标准分枝杆菌的色谱特征进行了研究，得到了特异性指纹图。并对４２株临床菌株进行了鉴别。     

Evaluation and validation of the ABI 3700, ABI 3100, and the MegaBACE 1000 capillary array electrophoresis instruments for use with short tandem repeat microsatellite typing in a forensic environment

The demand for high-throughput DNA profiling has increased with the introduction of national DNA databases and has led to the development of automated methods of short tandem repeat (STR) profile production; however, a potential bottleneck still exists at the gel electrophoresis stage. Capillary electrophoresis sequencers capable of processing 96 samples with considerably reduced manual intervention are now available. In this paper, we compare the ABI Prism 377 slab-gel sequencer currently used by the Forensic Science Service with three leading capillary array electrophoresis instruments: the ABI Prism 3700, the Amersham MegaBACE 1000 and the 16-capillary ABI Prism 3100. We describe the experiments used to evaluate and validate these platforms for forensic use with the STR multiplex Ampf/STR SGMplus [1, 2], along with comparative data from the ABI Prism 377 sequencer.     

Capillary liquid chromatographic fingerprint used for discrimination of Zingiber montanum from related species

Fingerprint analysis using capillary liquid chromatography (CLC) has been developed for discrimination of Zingiber montanum (ZM) from related species, for example Z. americans (ZA) and Z. zerumbet (ZZ). By comparing the fingerprint chromatograms of ZM, ZA, and ZZ we could identify ZM samples and discriminate them from ZA and ZZ by using their marker peaks. We also combined CLC fingerprint with multivariate analysis, including principal-component analysis (PCA) and canonical variate analysis (CVA); all three species were discriminated successfully. This result indicates that CLC fingerprint analysis in combination with PCA and CVA can be used for discrimination of ZM samples from samples of related species.

Oil-spill identification by gas chromatography-mass spectrometry

Two approaches are proposed for the identification of a contaminant caused by the spilling of oil or oil products in water. A capillary gas chromatography (CGC)-mass spectrometry (MS) method for oil spill identification is applied. The presented approaches describe the use of MS data of 18 selective ions of spilled product and the probable pollutant. The spill identification is accomplished on the bases of a quantitative comparison between the ion chromatograms of the samples taken from the probable pollutant and from the spill itself. The other approach is made by chemometric treatment of complete CGC-MS data.     

Capillary column gas chromatographic identification of sugars in honey as trimethylsilyl derivatives

A method for identifying carbohydrates (mono-, di- and trisaccharides) in honey is presented. It is based on the separate preparation of both trimethylsilyl ethers and oxime trimethylsilyl ethers of the sugars followed by their gas chromatographic separation on a fused-silica capillary column coated with OV-101 using temperature programming. From the two chromatograms, the number of peaks given by each derivatized sugar, their relative retention times and peak-area ratios are used for identification. The identities of two unidentified trisaccharide peaks are considered. Quantitative applications to honey sugar analysis are discussed.     

Detailed analysis and group-type separation of natural fats and oils using comprehensive two-dimensional gas chromatography

Comprehensive gas chromatography (GC x GC) is an adequate methodology for the separation and identification of very complex samples. It is based on the coupling of two capillary columns that each give a different but substantial contribution to the unprecedented resolving power of this technique. The 2D space chromatograms that derive from GC x GC analysis have great potential for identification. This is due to the fact that the contour plot positions, pinpointed by two retention time coordinates, give characteristic patterns for specific families of compounds that can be mathematically translated. This investigation concerned the application of this principle to fatty acid methyl esters that were grouped on an equal double bond number basis. The ester samples were derived from various lipids and all underwent bidimensional analysis on two sets of columns. Peak attribution was supported by mass spectra, linear retention indices and information reported in the literature.     

Determination of nine active components in Radix Hedysari and Radix Astragali using capillary HPLC with diode array detection and MS detection

A capillary HPLC (cHPLC) coupled with diode array detection (DAD) and MS method was developed for the simultaneously qualitative and quantitative determination of nine components, namely vanillic acid, calycosin-7-O-beta-D-glucoside, (6alphaR,11alphaR)-9,10-dimethoxypterocarpan-3-O-beta-D-glucoside, ononin, calycosin, (3R)-2'-hydroxy-3',4'-dimethoxyisoflavan-7-O-beta-D-glucoside, isoliquiritigenin, formononetin, (3R)-8,2'-dihydroxy-7,4'-dimethoxyisoflavan, in Radix Hedysari (Hongqi) and Radix Astragali (Huangqi). Simultaneous separation of these nine compounds was achieved on a Zorbax C18 microcolumn (5 microm, 150 x 0.3 mm). The mobile phase consisted of (A) 0.3% aqueous formic acid and (B) ACN with a gradient elution. The identification of nine compounds in both Hongqi and Huangqi was confirmed by TOF-MS. All calibration curves showed good linearity (R(2) >0.998) within test ranges. This method showed good repeatability for the quantification of these nine components in Hongqi and Huangqi with intra- and inter-day variations of less than 1.89 and 3.13%, respectively. The validated method was successfully applied to quantify nine investigated components in eighteen samples of Hongqi and Huangqi. Hierarchical cluster analysis of 18 samples was performed using the peak area of nine analytes on cHPLC chromatograms. The result showed that Hongqi and Huangqi are significantly different, though the two species of Astragalus are very similar.     

UPLC-UV-MSE analysis for quantification and identification of major carotenoid and chlorophyll species in algae

A fast method for quantification and identification of carotenoid and chlorophyll species utilizing liquid chromatography coupled with UV detection and mass spectrometry has been demonstrated and validated for the analysis of algae samples. This method allows quantification of targeted pigments and identification of unexpected compounds, providing isomers separation, UV detection, accurate mass measurements, and study of fragment ions for structural elucidation in a single run. This is possible using parallel alternating low- and high-energy collision spectral acquisition modes, which provide accurate mass full scan chromatograms and accurate mass high-energy chromatograms. Here, it is shown how this approach can be used to confirm carotenoid and chlorophyll species by identification of key diagnostic fragmentations during high-energy mode. The developed method was successfully applied for the analysis of Dunaliella salina samples during defined red LED lighting growth conditions, identifying 37 pigments including 19 carotenoid species and 18 chlorophyll species, and providing quantification of 7 targeted compounds. Limit of detections for targeted pigments ranged from 0.01?ng/mL for lutein to 0.24?ng/mL for chlorophyll a. Inter-run precision ranged for of 3 to 24 (RSD%) while inter-run inaccuracy ranged from ?17 to 11.

Analysis of natural red dyes (cochineal) in textiles of historical importance using HPLC and multivariate data analysis

A new analytical approach based on high-performance liquid chromatography with diode array detector (HPLC-DAD) and multivariate data analysis was applied and assessed for analyzing the red dye extracted from cochineal insects, used in precious historical textiles. The most widely used method of analysis involves quantification of specific minor compounds (markers), using HPLC-DAD. However, variation in the cochineal markers concentration, use of aggressive dye extraction methods and poor resolution of HPLC chromatograms can compromise the identification of the precise insect species used in the textiles. In this study, a soft extraction method combined with a new dye recovery treatment was developed, capable of yielding HPLC chromatograms with good resolution, for the first time, for historical cochineal-dyed textiles. After principal components analysis (PCA) and mass spectrometry (MS), it was possible to identify the cochineal species used in these textiles, in contrast to the accepted method of analysis. In order to compare both methodologies, 7 cochineal species and 63 historical cochineal insect specimens were analyzed using the two approaches, and then compared with the results for 15 historical textiles in order to assess their applicability to real complex samples. The methodology developed here was shown to provide more accurate and consistent information than the traditional method. Almost all of the historical textiles were dyed with Porphyrophora sp. insects. These results emphasize the importance of adopting the proposed methodology for future research on cochineal (and related red dyes). Mild extraction methods and HPLC-DAD/MSⁿ analysis yield distinctive profiles, which, in combination with a PCA reference database, are a powerful tool for identifying red insect dyes.     

An 18 Multi-InDels panel for analysis of highly degraded forensic biological samples

DNA genotyping from trace and highly degraded biological samples is one of the most significant challenges of forensic DNA identification. There is a lack of simple and effective methods for genotyping highly degraded samples. In this study, a multiple loci insertion/deletion polymorphisms (Multi-InDels) panel was designed for detecting 18 autosomal Multi-InDels through capillary electrophoresis (CE) with amplicon sizes no longer than 125 bp. Studies of sensitivity, degradation, and species specificity were performed and a population study was carried out using 192 samples from Han populations in Hunan province in the south of China. The combined random match probability (CMP) of these 18 Multi-InDels was 3.23 × 10^–12 and the cumulative probability of exclusion (CPE) was 0.9989, suggesting this panel could be used independently for human identification and could provide efficient supporting information for parentage testing. Complete profiles were obtained from as low as 62.5 pg of total input DNA after increasing the number of PCR cycles. Moreover, all alleles were detected from artificially highly degraded DNA after 80 min of boiling water bath treatment. This 18 Multi-InDels panel is simple, fast, and effective for the forensic analysis of highly degraded DNA.     

Discovery of neurosteroid glucuronides in mouse brain

Neurosteroid glucuronides were found for the first time in brain samples. The intact glucuronides were extracted from the cortex, hippocampus, hypothalamus, and mid-brain tissues of nicotine- and water-treated mice, and detected with capillary liquid chromatography-electrospray-tandem mass spectrometry (CapLC-ESI-MS/MS). The glucuronides of estradiol, cortisol, corticosterone, tetrahydrodeoxycorticosterone, pregnenolone, and isopregnanolone were identified by comparing retention times in selected reaction monitoring (SRM) chromatograms and the relative abundances of two SRM transitions of each neurosteroid glucuronide between the reference and authentic samples, thus providing reliable identification. In vitro experiments, carried out by using S9 fractions from mouse and rat brains, showed a formation of glucuronides with selected test compounds (corticosterone, pregnenolone, and dehydroepiandrosterone), suggesting that biosynthesis of neurosteroid glucuronides is possible in rodent brain.     

Speciation of magnesium in rat plasma using capillary electrophoresis-inductively coupled plasma-atomic emission spectrometry

A new method for speciation analysis of magnesium species and quantification of free magnesium concentrations in rat plasma was developed by on-line coupling of CE with inductively coupled plasma-atomic emission spectrometry (ICP-AES). Baseline separation of seven magnesium species was achieved by using a 120 cm (100 microm internal diameter) fused-silica capillary, a 20 kV separation voltage and a solution of 50 mmol/L NaAc-HAc (pH 5.5) as electrolyte buffer. CE-ICP-AES analysis of a rat plasma sample showed the presence of seven magnesium species, one of which was identified as free Mg2+ ion by spiking a Mg2+ standard; the migration time of the Mg2+ peak in the standard and the spiked sample matched with each other. One protein-bound magnesium species in rat plasma is associated with albumin, and the other three species are combined with globulin. The concentration of free magnesium in the plasma was 14.0 mg/L. The other six magnesium species were estimated to be 4-15 mg/L. RSDs of migration time and peak area for the magnesium species from ten replicates were less than 5%. The developed method was also applied to speciation analysis of magnesium species in spiked plasma samples. The recoveries of the free magnesium species in four samples ranged from 95.8 to 103.8%.     

DNA purification from crude samples for human identification using gradient elution isotachophoresis

Gradient elution isotachophoresis (GEITP) was demonstrated for DNA purification, concentration, and quantification from crude samples, represented here by soiled buccal swabs, with minimal sample preparation prior to human identification using STR analysis. During GEITP, an electric field applied across leading and trailing electrolyte solutions resulted in isotachophoretic focusing of DNA at the interface between these solutions, while a pressure‐driven counterflow controlled the movement of the interface from the sample reservoir into a microfluidic capillary. This counterflow also prevented particulates from fouling or clogging the capillary and reduced or eliminated contamination of the delivered DNA by PCR inhibitors. On‐line DNA quantification using laser‐induced fluorescence compared favorably with quantitative PCR measurements and potentially eliminates the need for quantitative PCR prior to STR analysis. GEITP promises to address the need for a rapid and robust method to deliver DNA from crude samples to aid the forensic community in human identification.     

Fast gradient elution reversed-phase liquid chromatography with diode-array detection as a high-throughput screening method for drugs of abuse. II. Data analysis

In Part I of this work, we developed a method for the detection of drugs of abuse in biological samples based on fast gradient elution liquid-chromatography coupled with diode array spectroscopic detection (LC-DAD). In this part of the work, we apply the chemometric method of target factor analysis (TFA) to the chromatograms. This algorithm identifies the target compounds present in chromatograms based on a spectral library, resolves nearly co-eluting components, and differentiates between drugs with similar spectra. The ability to resolve highly overlapped peaks using the spectral data afforded by the DAD is what distinguishes the present method from conventional library searching methods. Our library has a mean list length (MLL) of 1.255 and a discriminating power of 0.997 when both retention index and spectral factors are considered. The algorithm compares a library of 47 different compounds of toxicological relevance to unknown samples and identifies which compounds are present based on spectral and retention index matching. The application of a corrected retention index for identification rather than raw retention times compensates for long-term and column-to-column retention time shifts and allows for the use of a single library of spectral and retention data. Training data sets were used to establish the search and identification parameters of the method. A validation data set of 70 chromatograms was used to calculate the sensitivity (correct identification of positives) and specificity (correct identification of negatives) of the method, which were found to be 92% and 94%, respectively.     

Stronger together: Analytical techniques for recombinant adeno associated virus

With recent FDA approval of two recombinant adeno-associated virus (rAAV)-based gene therapies, these vectors have proven that they are suitable to address monogenic diseases. However, rAAVs are relatively new modalities, and their production and therapy costs significantly exceed those of conventional biologics. Thus, significant efforts are made to improve the processes, methods, and techniques used in manufacturing and quality control (QC). Here, we evaluate transmission electron microscopy (TEM), analytical ultracentrifugation (AUC), and two modes of capillary electrophoresis (CE) for their ability to analyze the DNA encapsidated by rAAVs. While TEM and AUC are well-established methods for rAAV, capillary gel electrophoresis (CGE) has been just recently proposed for viral genome sizing. The data presented reflect that samples are very complex, with various DNA species incorporated in the virus, including small fragments as well as DNA that is larger than the targeted transgene. CGE provides a good insight in the filling of rAAVs, but the workflow is tedious and the method is not applicable for the determination of DNA titer, since a procedure for the absolute quantification (e.g., calibration) is not yet established. For estimating the genome titer, we propose a simplified capillary zone electrophoresis approach with minimal sample preparation and short separation times (<5 min/run). Our data show the benefits of using the four techniques combined, since each of them alone is prone to delivering ambiguous results. For this reason, a clear view of the rAAV interior can only be provided by using several analytical methods simultaneously.     

Gel-permeation chromatography. V. A study of “overloading effects”

In the calculation of molecular weight averages from GPC chromatograms and in the correction for zone broadening effects, it is assumed that the retention volumes of the individual species are not affected by the presence of the other components in the sample (linear fractionation process). This assumption was tested by the computer comparisons of the chromatograms of mixtures of narrow molecular weight distribution polystyrene standards and the envelopes of the individual chromatograms of the components of the mixtures. Disagreements between experimental and computer synthesized chromatograms were interpreted as non-linear fractionation effects. The investigation covered a range of molecular weights (1.8 × 10⁶ to 2100), molecular weight distributions (binary and seven component mixtures), and sample loadings (2 to 70 mg). Accurate normalizations of raw GPC chromatograms and calculations of molecular weight averages were made possible through an automated GPC apparatus using a high-speed computer for data acquisition and data reduction. It was found that some nonlinear fractionation effects (large disagreement between chromatograms of the mixture and the computed envelopes of the individual chromatograms of the components of the mixture) became more pronounced as sample loading was increased and as the molecular weight distribution of the sample narrows. The nonlinear effect was also found to be sensitive to the molecular weight of the sample.