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At least 1,225 records · Page 68Linked to original sources
PubMed2005

A modified automated high-throughput mycobacterial interspersed repetitive unit method for genotyping Mycobacterium tuberculosis.

A total of 502 isolates of Mycobacterium tuberculosis collected in Taiwan were genotyped using a modified and high-throughput typing system involving mycobacterial interspersed repetitive units. The Hunter-Gaston discriminatory index improved significantly to 0.972 with the modified 15-locus scheme, including ETR-A, ETR-B, and ETR-C, compared with 0.951 for the previously reported 12-locus design.

Bacterial Typing Techniques↗
PubMed2004

Detection of influenza B in clinical specimens: comparison of high throughput RT-PCR and culture confirmation.

Influenza virus is one of the major causes of worldwide respiratory tract infections during the winter season. Here we describe a high throughput (HTP) protocol for rapid diagnosis of influenza B that combines automated viral RNA extraction with detection and quantification by TaqMan-based PCR. Using this methodology, we tested 4176 nasal swabs collected from children enrolled in a European influenza vaccine trial during the winter of 2000 to compare our HTP PCR method to culture confirmation for detection of influenza B. Among these, 37 were positive by culture and 169 were positive by PCR irrespective of virus copy number. However, when specimens with fewer than 20 copies of the viral genome were disregarded, a good correlation between two methods was observed. At this cut-off, 34 specimens were positive and 4106 were negative by both methods. Statistical analysis of the data using culture confirmation as the standard indicated that the sensitivity of HTP RT-PCR for influenza B was 92% (95% CI, 0.83-1), and the specificity was 99% (95% CI, 0.99-1). In summary, HTP RT-PCR was proved to be more rapid and sensitive than culture confirmation, and it correlated significantly with culture confirmation for specimens containing more than 20 copies of the viral genome.

Animals↗
PubMed2003

Membrane protein structural biology: the high throughput challenge.

Membrane proteins represent roughly one-third of the proteins encoded in the genome, yet fewer than 1% of the proteins are of known structure. High-throughput crystallography offers the hope of correcting this imbalance. In order for large-scale membrane protein structural biology to realize its full promise, however, significant technical challenges must be overcome, the two most substantial being facile protein overexpression and reliable methods for crystal growth.

Cloning, Molecular↗
PubMed2004

Model selection and optimal sampling in high-throughput experimentation.

The practical difficulties encountered in analyzing the kinetics of new reactions are considered from the viewpoint of the capabilities of state-of-the-art high-throughput systems. There are three problems. The first problem is that of model selection, i.e., choosing the correct reaction rate law. The second problem is how to obtain good estimates of the reaction parameters using only a small number of samples once a kinetic model is selected. The third problem is how to perform both functions using just one small set of measurements. To solve the first problem, we present an optimal sampling protocol to choose the correct kinetic model for a given reaction, based on T-optimal design. This protocol is then tested for the case of second-order and pseudo-first-order reactions using both experiments and computer simulations. To solve the second problem, we derive the information function for second-order reactions and use this function to find the optimal sampling points for estimating the kinetic constants. The third problem is further complicated by the fact that the optimal measurement times for determining the correct kinetic model differ from those needed to obtain good estimates of the kinetic constants. To solve this problem, we propose a Pareto optimal approach that can be tuned to give the set of best possible solutions for the two criteria. One important advantage of this approach is that it enables the integration of a priori knowledge into the workflow.

Journal Article↗
PubMed2003

Fluorescence resonance energy transfer (FRET) as a high-throughput assay for coupling reactions. Arylation of amines as a case study.

A solution-phase assay based on fluorescence resonance energy transfer (FRET) was developed for high-throughput screening of palladium catalyzed aminations of aryl halides. Dansylpiperazine was used as the fluorescent component and a chloro- or bromoarene tagged with an azodye as the quenching partner. Fluorescence intensities of reaction aliquots correlated linearly with reaction yield after dilution to appropriate concentrations. A library of 119 phosphine and heterocyclic carbene ligands was evaluated in duplicate reactions of two combinations. In general, the FRET assay displayed excellent reproducibility, with less than 5% of the duplicate experiments showing significant variability in yields. Among reactions producing greater than 50% yield, the average percent uncertainty was just 5%. For a small subset of sterically hindered ligands, differences in yields between 10 and 20% were observed between the substrates bearing dyes for the FRET assay and substrates that are unfunctionalized. However, the remaining catalyst combinations gave yields similar to those expected from literature precedent. In addition to an evaluation of the accuracy of the FRET assay, this work includes the use of the FRET assay to investigate relative activities of various catalysts for the amination of aryl bromides and chlorides and to find conditions for aminations in more polar solvents. Reactions with K(3)PO(4) base in aqueous mixtures of polar and nonpolar organic solvents were shown to be appropriate for the amination chemistry.

Amines↗
PubMed2005

Using enzyme inhibition as a high throughput method to measure the enantiomeric excess of a chiral sulfoxide.

[reaction: see text] The enantiomeric excess of methyl p-tolyl sulfoxide can be determined in a high throughput format by measuring its ability to inhibit the alcohol dehydrogenase catalyzed oxidation of ethanol. The two enantiomers of the sulfoxide have very different inhibition constants for the enzyme. Thus, the initial rate of ethanol oxidation in the presence of the sulfoxide is correlated with the sulfoxide enantiomeric excess.

Ethanol↗
PubMedDate not supplied

The use of high-throughput synthesis and purification in the preparation of a directed library of adrenergic agents.

A library of potential agonists and antagonists for adrenergic receptors was prepared using high-throughput solution-phase parallel synthesis. Traditional solution-phase reductive amination reactions followed by rapid purification by ion exchange chromatography yielded products with near-analytical purity. An array of ketones and amines, arranged in an 8 x 12 matrix, were combined to form 96 individual compounds.

Adrenergic Agonists↗
PubMed2002

High throughput screening of human subtelomeric DNA for copy number changes using multiplex amplifiable probe hybridisation (MAPH).

BACKGROUND: Subtelomeric regions of the human genome are gene rich, with a high level of sequence polymorphism. A number of clinical conditions, including learning disability, have been attributed to subtelomeric deletions or duplications, but screening for deletion in these regions using conventional cytogenetic methods and fluorescence in situ hybridisation (FISH) is laborious. Here we report that a new method, multiplex amplifiable probe hybridisation (MAPH), can be used to screen for copy number at subtelomeric regions. METHODS: We have constructed a set of MAPH probes with each subtelomeric region represented at least once, so that one gel lane can assay copy number at all chromosome ends in one person. Each probe has been sequenced and, where possible, its position relative to the telomere determined by comparison with mapped clones. RESULTS: The sensitivity of the probes has been characterised on a series of cytogenetically verified positive controls and 83 normal controls were used to assess the frequency of polymorphic copy number with no apparent phenotypic effect. We have also used MAPH to test a cohort of 37 people selected from males referred for fragile X syndrome testing and found six changes that were confirmed by dosage PCR. CONCLUSIONS: MAPH can be used to screen subtelomeric regions of chromosomes for deletions and duplications before confirmation by FISH or dosage PCR. The high throughput nature of this technique allows it to be used for large scale screening of subtelomeric copy number, before confirmation by FISH. In practice, the availability of a rapid and efficient screen may allow subtelomeric analysis to be applied to a wider selection of patients than is currently possible using FISH alone.

Analysis of Variance↗
PubMed2002

Determination of ligand-MurB interactions by isothermal denaturation: application as a secondary assay to complement high throughput screening.

We used a temperature-jump isothermal denaturation procedure with various methods of detection to evaluate the quality of putative inhibitors of MurB discovered by high-throughput screening. Three optical methods of detection-ultraviolet hyperchromicity of absorbance, fluorescence of bound dyes, and circular dichroism-as well as differential scanning calorimetry were used to dissect the effects of two chemical compounds and a natural substrate on the enzyme. The kinetics of the denaturation process and binding of the compounds detected by quenching of flavin fluorescence were used to quantitate the dose dependencies of the ligand effects. We found that the first step in the denaturation of MurB is the rapid loss of flavin from the active site and that the two chemical inhibitors appeared to destabilize the interaction of the cofactor with the enzyme but stabilize the global unfolding. The kinetics of the denaturation process as well as the loss of flavin fluorescence on binding established that both compounds had nanomolar affinities for the enzyme. We showed that coupling of the various detection methods with isothermal denaturation yields a powerful regimen to provide analytical data for assessing inhibitor specificity for a protein target.

Automation↗
PubMed2003

A modular, fully integrated ultra-high-throughput screening system based on confocal fluorescence analysis techniques.

The rapid increase in size of compound libraries, as well as new targets emerging from the Human Genome Project, require progress in ultra-high-throughput screening (uHTS) systems. In a joint effort with scientists and engineers from the biotech and the pharmaceutical industry, a modular, fully integrated system for miniaturized uHTS was developed. The goal was to achieve high data quality in small assay volumes (1-4 microL) combined with reliable and unattended operation. Two new confocal fluorescence readers have been designed. One of the instruments is a 4-channel confocal fluorescence reader, measuring with 4 objectives in parallel. The fluorescence readout is based on single-molecule detection methods, allowing high sensitivity at low tracer concentrations and delivering an information-rich output. The other instrument is a confocal fluorescence imaging reader, where the images are analyzed in terms of generic patterns and quantified in units of intensity per pixel. Both readers are spanning the application range from assays with isolated targets in homogenous solution or membrane vesicle-based assays (4-channel reader) to cell-based assays (imaging reader). Results from a comprehensive test on these assay types demonstrate the high quality and robustness of this screening system.

Anti-Bacterial Agents↗
PubMed2004

High-throughput analysis of human serum for selected polychlorinated biphenyls (PCBs) by gas chromatography-isotope dilution time-of-flight mass spectrometry (GC-IDTOFMS).

A method for the high-throughput analysis of human serum for the 38 most prevalent polychlorinated biphenyls (PCBs) based on the use of fast gas chromatography-isotopic dilution time-of-flight mass spectrometry (GC-IDTOFMS) is presented. The chromatographic separation time was 8 min. The separation of the congeners was carried out either chromatographically or analytically using the mass spectral deconvolution capability of the TOFMS. The instrument and the method limits of detection (LODs) were 0.5 pg microL(-1) and 20 pg microL(-1), respectively, which is not as good as the one achieved using high resolution mass spectrometry (HRMS) but allows the detection and quantification of the prevalent PCBs present in real human serum samples. The dynamic range covered 3 orders of magnitude. The comparison with the high resolution mass spectrometry (HRMS) reference method (28 min) was good and some separation improvements have been observed. This method allows the analysis of 100 samples per day per instrument.

Environmental Monitoring↗
PubMedDate not supplied

High-throughput microcoil NMR of compound libraries using zero-dispersion segmented flow analysis.

An automated system for loading samples into a microcoil NMR probe has been developed using segmented flow analysis. This approach enhanced 2-fold the throughput of the published direct injection and flow injection methods, improved sample utilization 3-fold, and was applicable to high-field NMR facilities with long transfer lines between the sample handler and NMR magnet. Sample volumes of 2 microL (10-30 mM, approximately 10 microg) were drawn from a 96-well microtiter plate by a sample handler, then pumped to a 0.5-microL microcoil NMR probe as a queue of closely spaced "plugs" separated by an immiscible fluorocarbon fluid. Individual sample plugs were detected by their NMR signal and automatically positioned for stopped-flow data acquisition. The sample in the NMR coil could be changed within 35 s by advancing the queue. The fluorocarbon liquid wetted the wall of the Teflon transfer line, preventing the DMSO samples from contacting the capillary wall and thus reducing sample losses to below 5% after passage through the 3-m transfer line. With a wash plug of solvent between samples, sample-to-sample carryover was <1%. Significantly, the samples did not disperse into the carrier liquid during loading or during acquisitions of several days for trace analysis. For automated high-throughput analysis using a 16-second acquisition time, spectra were recorded at a rate of 1.5 min/sample and total deuterated solvent consumption was <0.5 mL (1 US dollar) per 96-well plate.

Combinatorial Chemistry Techniques↗
PubMed2004

High-throughput liquid chromatography for drug analysis in biological fluids: investigation of extraction column life.

A novel method was developed and assessed to extend the lifetime of extraction columns of high-throughput liquid chromatography (HTLC) for bioanalysis of human plasma samples. In this method, a 15% acetic acid solution and 90% THF were respectively used as mobile phases to clean up the proteins in human plasma samples and residual lipids from the extraction and analytical columns. The 15% acetic acid solution weakens the interactions between proteins and the stationary phase of the extraction column and increases the protein solubility in the mobile phase. The 90% THF mobile phase prevents the accumulation of lipids and thus reduces the potential damage on the columns. Using this novel method, the extraction column lifetime has been extended to about 2000 direct plasma injections, and this is the first time that high concentration acetic acid and THF are used in HTLC for on-line cleanup and extraction column lifetime extension.

Acetic Acid↗
PubMed2002

High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization.

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, and miscarriages. Automated detection of subtle deletions or duplications involving telomeres is essential for high-throughput diagnosis, but impossible when conventional cytogenetic methods are used. Array-based comparative genomic hybridization (CGH) allows high-resolution screening of copy number abnormalities by hybridizing differentially labeled test and reference genomes to arrays of robotically spotted clones. To assess the applicability of this technique in the diagnosis of (sub)telomeric imbalances, we here describe a blinded study, in which DNA from 20 patients with known cytogenetic abnormalities involving one or more telomeres was hybridized to an array containing a validated set of human-chromosome-specific (sub)telomere probes. Single-copy-number gains and losses were accurately detected on these arrays, and an excellent concordance between the original cytogenetic diagnosis and the array-based CGH diagnosis was obtained by use of a single hybridization. In addition to the previously identified cytogenetic changes, array-based CGH revealed additional telomere rearrangements in 3 of the 20 patients studied. The robustness and simplicity of this array-based telomere copy-number screening make it highly suited for introduction into the clinic as a rapid and sensitive automated diagnostic procedure.

Chromosome Aberrations↗
PubMed2000

Development of a homogeneous time-resolved fluorescence assay for high throughput screening to identify Lck inhibitors: comparison with scintillation proximity assay and streptavidin-coated plate assay.

This study details the development of a homogeneous time-resolved fluorescence (HTRF) high throughput screening assay to identify inhibitors of Lck. HTRF was compared with scintillation proximity and streptavidin-coated plate assays. Because of the differences in the sensitivity of detection of phosphotyrosine among the three assays, different amounts of enzyme were used. However, the concentrations of the other assay components were standardized. When using similar assay conditions, the calculated IC(50) values of inhibitory compounds were independent of assay format. Furthermore, filtration experiments revealed that phosphorylation of a biotinyl poly-Glu,Ala, Tyr peptide substrate was less than autophosphorylation of the Lck enzyme; this was due to the low K(m) value for biotinyl poly-Glu,Ala,Tyr. In the HTRF assay, small amounts of enzyme and high concentrations of ATP could be used, thereby minimizing the effects of autophosphorylation. Higher ATP concentration would also minimize the effect of ATP competitors. Using this technology, it may be possible to find novel kinase inhibitors that do not act at the ATP binding site of protein tyrosine kinases.

Biotin↗
PubMed2001

High-throughput semi-automated 96-well liquid/liquid extraction and liquid chromatography/mass spectrometric analysis of everolimus (RAD 001) and cyclosporin a (CsA) in whole blood.

A semi-automated high-throughput liquid/liquid extraction (LLE) assay was developed for RAD001 and cyclosporin A (CsA) in human blood. After addition of internal standard and ammonium hydroxide, samples were extracted twice with methyl tert-butyl ether (MTBE). The organic extract was evaporated to dryness and reconstituted in mobile phase. Where possible, sample transfer and LLE steps were automated using a Tomtec Quadra 96 workstation. Samples were analyzed using ESI-LC/MS/MS employing the transitions of ([M + NH(4)](+) --> [M + H](+)) for CsA and ([M + NH(4)](+) --> [M + H-(CH(3)OH + H(2)O)](+)) for RAD001, under isocratic chromatographic conditions (75:25, (v/v), acetonitrile/20 mM ammonium acetate) with a run time of 3.6 min. A lower limit of quantitation (LLOQ) of 0.368 ng/mL and 5.23 ng/mL was achieved for RAD001 and CsA, respectively, using a sample volume of 0.3 mL for the analysis. The method was validated over a 3-day period and the resulting calibration curves had a correlation coefficient >0.99 over the concentration range 0.368 to 409 ng/mL and 5.24 to 1748 ng/mL for RAD001 and CsA, respectively. The inter-day coefficient of variation (CV) was less than 15% at the LLOQ for both compounds. The method was applied to the analysis of clinical samples. Under normal working conditions four 96-well plates could be extracted and LC/MS analysis completed in less than 28 h. A marked improvement in sample throughput efficiency was realized with this LLE method when compared to existing solid phase extraction (SPE) methods which deal with both RAD001 and CsA.

Chromatography, Liquid↗
PubMed2004

High-throughput liquid chromatography-tandem mass spectrometry determination of bupropion and its metabolites in human, mouse and rat plasma using a monolithic column.

In the present work, a high-throughput LC/MS/MS method using a Chromolith RP-18 (50 mm x 4.6 mm) monolithic column was developed and partially validated for the determination of bupropion (BUP), an anti-depressant drug, and its metabolites, hydroxybupropion and threo-hydrobupropion (TB), in human, mouse, and rat plasma. A modern integrated liquid chromatograph and an LC/MS/MS system with a TurboIonSpray (TIS) interface were used for the positive electrospray selected reaction monitoring (SRM) LC/MS analyses. Spiked control plasma calibration standards and quality control (QC) samples were extracted by semi-automated 96-well liquid-liquid extraction (LLE) using ethyl acetate. A mobile phase consisting of 8mM ammonium acetate-acetonitrile (55:45, v/v) delivered isocratically at 5 ml/min, and split post-column to 2 ml/min directed to the TIS, provided the optimum conditions for the chromatographic separation of bupropion and its metabolites within 23s. The isotope-labeled D(6)-bupropion and D(6)-hydroxybupropion were used as internal standards. The method was linear over a concentration range of 0.25-200 ng/ml (bupropion and threo-hydrobupropion), and 1.25-1000 ng/ml (hydroxybupropion). The intra- and inter-day assay accuracy and precision were within 15% for all analytes in each of the biological matrices. The monolithic column performance as a function of column backpressure, peak asymmetry, and retention time reproducibility was adequately maintained over 864 extracted plasma injections.

Animals↗
PubMed2004

High-throughput sample preparation procedures for the quantitation of a new bone integrin alpha(nu)beta(3) antagonist in human plasma and urine using liquid chromatography-tandem mass spectrometry.

High throughput LC-MS/MS assays to quantitate a new alpha(nu)beta(3) bone integrin antagonist (I) in human plasma and urine have been developed using instruments programmed to automate sample preparation procedures. Packard liquid handling system-MultiPROBE II EX was programmed for preparing calibration standards in control plasma and urine, acidifying all standards, quality control (QC), and clinical samples with necessary dilutions, and adding the internal standard to the acidified samples. TOMTEC Quadra 96 was programmed to perform the solid phase extraction (SPE) process on a 3M 96-well mixed phase cation standard density (MPC-SD) plate to isolate the analytes from the sample matrix. The extract collected from both types of matrices was directly injected into reversed-phase LC-MS/MS system with a Turbo Ion Spray (TIS) interface in the positive ionization mode. The plasma and urine assays have the calibration range of 0.5-1500 and 2-6000 ng/mL, respectively. Validation of the automated and the manual plasma assays showed that application of MultiPROBE II to sample preparation gave comparable accuracy and precision. Overall, the automated approaches with minimum manual intervention enhanced the throughput of sample preparation.

Bone and Bones↗