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At least 1,009 records · Page 56Linked to original sources
PubMed1999

High-throughput genotyping method for glutathione S-transferase T1 and M1 gene deletions using TaqMan probes.

A high-throughput genotyping method has been developed to detect gene deletion polymorphisms of glutathione-S-transferase theta and mu (GSTT1 and GSTM1). This method utilizes the 5'-nuclease activity of Taq polymerase in conjunction with fluorogenic TaqMan probes. In contrast to traditional allelic discrimination genotyping to detect single nucleotide polymorphisms, the current assay has been designed to detect gene deletion by utilizing custom-designed TaqMan probes in conjunction with an exogenous internal positive control probe. The TaqMan genotyping results were validated by a commonly used multiplex PCR technique. Screening of 71 unrelated individuals revealed gene deletion (null) genotype of 15.5% and 40.8% for GSTT1 and GSTM1, respectively. This TaqMan genotyping method is rapid, reproducible, and highly sensitive and could be applied toward fully automated large-scale genotyping.

Alleles↗
PubMed2006

High-throughput affinity ranking of antibodies using surface plasmon resonance microarrays.

A method was developed to rapidly identify high-affinity human antibodies from phage display library selection outputs. It combines high-throughput Fab fragment expression and purification with surface plasmon resonance (SPR) microarrays to determine kinetic constants (kon and koff) for 96 different Fab fragments in a single experiment. Fabs against human tissue kallikrein 1 (hK1, KLK1 gene product) were discovered by phage display, expressed in Escherichia coli in batches of 96, and purified using protein A PhyTip columns. Kinetic constants were obtained for 191 unique anti-hK1 Fabs using the Flexchip SPR microarray device. The highest affinity Fabs discovered had dissociation constants of less than 1 nM. The described SPR method was also used to categorize Fabs according to their ability to recognize an apparent active site epitope. The ability to rapidly determine the affinities of hundreds of antibodies significantly accelerates the discovery of high-affinity antibody leads.

Automation↗
PubMed2001

An integrated ten-pump, eight-channel parallel LC/MS system for automated high-throughput analysis of proteins.

An integrated 10-pump eight-channel LC/MS system has been developed for automated high-throughput analysis of intact proteins in recombinant protein purification processes. The key features of the system include (1) a compact 10-pump HPLC module that uses two pumps to generate a binary gradient and 8 pumps to deliver the mixed gradient to eight independent flow channels; (2) a TOF mass spectrometer with an eight-channel multiplexed ESI interface, which records separate data for all eight channels over each HPLC run cycle; and (3) highly automated data processing software that allows unattended calculation of protein molecular weight (in Da) from original mass spectral data (in m/z). This system was used in the routine screening of fractions from preparative scale chromatography to monitor the purification process with the required mass accuracy and throughput. As an example, the production and purification of an acylated protein with a molecular weight of 9 kDa is described. Using this off-line approach, it is practical to fully characterize protein-containing fractions from column chromatography with an overall analytical throughput of 1 min/protein sample with minimum operator involvement.

Autoanalysis↗
PubMed2007

Development of a homogeneous calcium mobilization assay for high throughput screening of mas-related gene receptor agonists.

AIM: To develop homogeneous calcium mobilization assay for high-throughput screening (HTS) of mas-related gene (Mrg) receptor agonists. METHODS: CHO-K1 cells stably expressing the full-length MrgD receptor and a calcium-sensitive dye were used to develop an HTS assay based on intracellular calcium influx. This method was applied to large-scale screening of a library containing 8000 synthetic compounds and natural product extracts. cAMP measurements were carried out to verify the bioactivities of the hits found by the calcium mobilization assay. Similar approaches were also employed in the identification of the MrgA1 receptor agonists following HTS of 16,000 samples. RESULTS: EC(50) values of the positive control compounds (beta-alanine for MrgD receptor and dynorphin A for MrgA1 receptor) determined by the calcium mobilization assay were consistent with those reported in the literature, and the Z' factors were 0.65 and 0.50 for MrgD and MrgA1 receptor assay, respectively. About 31 compounds for the MrgD receptor and 48 compounds for the MrgA1 receptor showing > or =20% of the maximal agonist activities found in the controls were initially identified as hits. Secondary screening confirmed that 2 compounds for each receptor possessed specific agonist activities. Intracellular cAMP level measurements indicated that the 2 confirmed hits displayed the functionality of the MrgD receptor agonists. CONCLUSION: A series of validation studies demonstrated that the homogeneous calcium mobilization assay developed was highly efficient, amenable to automation and a robust tool to screen potential MrgD and MrgA1 receptor agonists. Its application may be expanded to other G-protein coupled receptors that mobilize calcium influx upon activation.

Animals↗
PubMedDate not supplied

High-throughput capillary gas chromatography for the determination of polychlorinated biphenyls and fatty acid methyl esters in food samples.

High-throughput capillary gas chromatography (CGC) methods, developed during the Belgian 1999 "dioxin" food crisis, for the determination of the contaminating polychlorinated biphenyls (PCBs) and the fatty acid composition of the lipids are described. For PCB analysis, the fat obtained by ultrasonic extraction is fractionated by matrix solid-phase dispersion, and the PCBs are analyzed by CGC-electron capture detection on a 10-mL x 100-microm-i.d. HP-5MS column. Analytical conditions for the high-speed column are deduced from analyses on conventional CGC columns using the method translation software. The concept of retention time locking is implemented to facilitate the elucidation of the PCB markers. The fatty acid methyl esters (FAMEs) are prepared by the sodium methylate procedure on part of the ultrasonic extract followed by analysis on 10-mL x 100-microm-i.d. HP-WAX or BPX-70 capillary columns. By optimizing both the sample preparation and CGC analysis, the throughput is more than fifty PCB and FAME samples per day with the same robustness as conventional methods.

Chromatography, Gas↗
PubMed2003

Improved fluorogenic histone deacetylase assay for high-throughput-screening applications.

Histone deacetylases (HDACs) are key targets for chemotherapeutic intervention in malignant diseases. In this paper, a highly sensitive, nonisotopic, homogeneous assay for high-throughput screening of HDAC inhibitors is presented. The assay is based on a new fluorogenic peptidic substrate of HDACs comprising an epsilon-acetylated lysyl moiety and an adjacent 4-methylcoumarin-7-amide moiety at the C terminus of the peptide chain. Upon deacetylation of the acetylated lysyl moiety, molecules are recognized as substrates by trypsin, which releases highly fluorescent 7-amino-4-methylcoumarin molecules in a subsequent step of the assay. The fluorescence increase is directly proportional to the amount of deacetylated substrate molecules, i.e., HDAC activity. Validation of an improved version of the assay revealed (i) a significantly lower enzyme consumption, (ii) an increased screening window coefficient, (iii) a good tolerance toward organic solvents, and (iv) a good suitability for a whole range of different HDAC-like enzymes. The novel assay thus will expedite studies of HDAC-like enzymes and in vitro screening for drug discovery.

Acetylation↗
PubMed2000

High throughput on-line solid phase extraction/tandem mass spectrometric determination of paclitaxel in human serum.

The feasibility of high throughput on-line solid phase extraction/tandem mass spectrometry (SPE/MS/MS) is tested for target analysis of paclitaxel in human serum. The use of a dual Prospekt system, with parallel SPE and elution directly to the mass spectrometer, resulted in a cycle time of 80 seconds for the entire, fully automated assay. The assay proved to be linear from 1 to 1000 ng/mL. Cartridges packed with small sorbent particles functioned both as SPE cartridges and as short analytical columns.

Blood Chemical Analysis↗
PubMedDate not supplied

High-throughput determination of identity, purity, and quantity of combinatorial library members using LC/MS/UV/ELSD.

We have used a high-throughput LC/MS/UV/ELSD method to rapidly determine the absolute quantity and purity of 42 organic compounds from seven lead discovery libraries. A general calibration curve generated from a different set of 42 compounds with seven different scaffolds was used in this analysis. We have also studied 33 organic compounds with different molecular weight (MW) by LC/MS/UV/ELSD to investigate the effect of MW on ELSD response and the accuracy for purity and quantity measurement using UV(214) and ELSD. A general ELSD calibration curve from these compounds was also generated to quantify 42 library compounds. Purity measurement by ELSD underestimates the amounts of impurities due to a reduced ELSD response from smaller molecular weight impurities often produced in library synthesis. Absolute quantity determination by ELSD is more accurate (RSD 28%) than that by UV(214) (48%) using a calibration curve generated from the same set of compounds with diverse MWs. Error assessment for the measurement of absolute quantity of a class of commercial compounds and a class of representing reference compounds from seven diverse lead discovery libraries shows that structurally related compounds should be used to generate calibration curves to sustain smaller deviation.

Calibration↗
PubMed1999

A generic particle-based nonradioactive homogeneous multiplex method for high-throughput screening using microvolume fluorimetry.

We have developed a novel fluorescence-based homogeneous binding assay for high-throughput screening of chemical compounds. In this assay, a Cy5- or Cy5.5-labeled ligand binds to receptor immobilized on a particle, either a bead or a cell. The resulting localized signal can be detected by a modified microvolume fluorimeter (MVF). When a molecule which competes with the labeled ligand is present, the localized fluorescence on cells or beads is reduced. Image processing software enumerates events and analyzes fluorescence intensity. We describe MVF assays for the IL-1 and IL-5 receptors. Using synthetic peptides with a range of affinities for the IL-1 receptor, we obtained IC(50) data consistent with those determined by radioligand binding assays. Because the image processing software can discriminate among events with different diameters, we were able to develop a multiplex assay, in which the IL-1R and IL-5R assays were carried out in the same well with each receptor immobilized on a different size of bead. IC(50) values generated in the multiplex assay for ligands specific to each receptor were comparable to those determined independently. Finally, similar IC(50) values were obtained in a 16-microl volume in an 864-well plate. This homogeneous, nonradioactive, miniaturizable, and multiplex-capable assay holds much promise for screening of combinatorial libraries and compound collections.

Animals↗
PubMedDate not supplied

High-throughput investigation of osteoblast response to polymer crystallinity: influence of nanometer-scale roughness on proliferation.

A high-throughput method for analyzing cellular response to crystallinity in a polymer material is presented. Variations in crystallinity lead to changes in surface roughness on nanometer length scales, and it is shown that cells are exquisitely sensitive to these changes. Gradients of polymer crystallinity were fabricated on films of poly(L-lactic acid) using a gradient in annealing temperature. The resultant morphologies were characterized using an atomic force microscope. Root-mean-square (rms) roughness values ranging from 0.5 to 13 nm were created on a single sample. MC3T3-E1 osteoblastic cells were cultured for 1, 3 and 5 d, and the number of cells was measured using automated fluorescence microscopy. It is shown that the rate of proliferation on the smooth regions of the films is much greater than that on the rough regions, and a monotonic variation in rate is observed as a function of roughness. The critical rms roughness, above which a statistically significant reduction in rate of proliferation occurs, was approximately 1.1 nm. Fluorescence microscopy measurements on immunostained cells indicate there is no significant change in cell area, the number or type of adhesions formed, or the degree of actin polymerization. Results from enzyme-linked immunofluorescence assays indicated that there was no detectable change in adhesion protein accessibility, suggesting the cells directly respond to substrate topography. The use of the gradient library approach yielded the functional dependence of cell proliferation on nanometer-scale roughness and gave a sensitive estimate of the critical roughness for which a decrease in proliferation is observed.

3T3 Cells↗
PubMed2004

High throughput approaches in neuroscience.

Traditional approaches to understanding biological problems are now being advanced with the use of high throughput technologies, which analyse multiple samples simultaneously, or thousands of analytes in a single sample. The application of these technologies in neurochemistry and neuroscience is beginning to be explored and is assisting in the development of new models of drug action, neuroanatomical investigations, and in identifying molecular pathways involved in neurological and psychiatric disease. Tools such as microarray-based gene expression profiling and 2D and multidimensional proteomic methods are uncovering functional components to a wide variety of neuroscience paradigms and the application of these technologies is set to become standard in analysis.

Animals↗
PubMed2005

Sphingolipidomics: high-throughput, structure-specific, and quantitative analysis of sphingolipids by liquid chromatography tandem mass spectrometry.

Sphingolipids are a highly diverse category of compounds that serve not only as components of biologic structures but also as regulators of numerous cell functions. Because so many of the sphingolipids in a biological system are bioactive and are often closely related structurally and metabolically (for example, complex sphingolipids<-->ceramide<-->sphingosine<-->sphingosine 1-phosphate), to understand the role(s) of sphingolipids in a given context one must conduct a "sphingolipidomic" analysis-i.e., a structure-specific and quantitative measurement of all of these compounds, or at least all members of a critical subset. Liquid chromatography tandem mass spectrometry (LC MS/MS) is currently the only technology with the requisite structural specificity, sensitivity, quantitative precision, and relatively high-throughput capabilities for such analyses in small samples ( approximately 10(6) cells). This review describes a series of protocols that have been developed for the relatively rapid analysis of all of the molecular species from 3-ketosphinganines through sphingomyelins and some glycosphingolipids (including all the compounds that are presently regarded as sphingolipid "second messengers") using normal- and reverse-phase LC to separate isometric and isobaric species (such as glucosylceramides and galactosylceramides) in combination with triple quadrupole (for MS/MS) and hybrid quadrupole-ion trap (for MS3) mass spectrometry. Also discussed are some of the issues remaining to be resolved in the analysis of the full sphingolipidome.

Animals↗
PubMed1999

Evaluation of a high-throughput second antibody radiobinding assay for measuring IgA antibodies to human tissue transglutaminase.

We describe a novel high-throughput radiobinding assay for IgA antibodies to tissue transglutaminase (TG) which uses second antibody precipitation to isolate immune complexes. Using this assay, 24 of 25 patients with untreated coeliac disease (96%) and nine of 526 healthy blood donors (2%) had TG antibody levels above a threshold defined by the 97.5th centile of 347 schoolchildren. All patients and five of the nine blood donors with transglutaminase antibodies above this threshold were endomysial antibody (EMA) positive. Using this threshold, 410/445 (92%) routine clinical samples were concordant for TG antibodies and EMA, including 72 of 75 with EMA. TG antibodies above the 97.5th centile were found in 32 of 370 EMA negative samples, 15 of whom had anti-gliadin antibodies (AGA), histologically proven coeliac disease or partial villous atrophy. We conclude that this assay achieves a sensitivity and a specificity at least equivalent to those of EMA. It is technically simple and suitable for coeliac disease screening.

Adolescent↗
PubMed2005

High-throughput RNA interference screens in Drosophila tissue culture cells.

This chapter describes the method used to conduct high-throughput screening (HTs) by RNA interference in Drosophila tissue culture cells. It covers four main topics: (1) a brief description of the existing platforms to conduct RNAi-screens in cell-based assays; (2) a table of the Drosophila cell lines available for these screens and a brief mention of the need to establish other cell lines as well as cultures of primary cells; (3) a discussion of the considerations and protocols involved in establishing assays suitable for HTS in a 384-well format; and (A) a summary of the various ways of handling raw data from an ongoing screen, with special emphasis on how to apply normalization for experimental variation and statistical filters to sort out noise from signals.

Animals↗
PubMed2002

Multiplexed on-column protein digestion and capillary electrophoresis for high-throughput comprehensive peptide mapping.

A novel scheme based on multiplexed capillary electrophoresis (CE) has been developed for high-throughput, low-cost and comprehensive peptide mapping. Orthogonal peptide maps of the protein of interest were obtained by using multiple reaction conditions with three different enzymes (trypsin, pepsin, and chymotrypsin), and multiple separation conditions with six zone electrophoresis buffers and two micellar electrokinetic chromatography (MEKC) buffers. Fifteen nanoliters of two protein samples (beta-lactoglobulin A and beta-lactoglobulin B) were separately mixed on-column and digested independently at 37 degrees C for 10 min to produce peptides in a 20-capillary system. The resulting peptides were detected simultaneously at 214 nm by a photodiode array detector. The overall analysis time from reaction to detection was about 40 min.

Buffers↗
PubMedDate not supplied

Use of design of experiments to optimize high-throughput semipreparative LC and LC/MS methods.

This paper describes an investigation into decreasing the run time for high-throughput semipreparative RP-HPLC methods without compromising the resolution. Experimental design was used to devise a small set of experiments in which factors, including solvent flow rate, solvent/column temperature, at-column dilution, and run time were varied systematically. The results were analyzed by means of multiple regression and partial least squares to generate a model relating the factors to the results, showing which factors are important. The model was then used to determine the optimal conditions.

Journal Article↗
PubMedDate not supplied

An empirical process for the design of high-throughput screening deck filters.

A process for objective identification and filtering of undesirable compounds that contribute to high-throughput screening (HTS) deck promiscuity is described. Two methods of mapping hit promiscuity have been developed linking SMARTS-based structural queries with historical primary HTS data. The first compares an expected assay hit rate to actual hit rates. The second examines the propensity of an individual compound to hit multiple assays. Statistical evaluation of the data indicates a correlation between the resultant functional group filters and compound promiscuity. These data corroborate a number of commonly applied filters as well as producing some unexpected results. Application of these models to HTS collection triage reduced the number of in-house compounds considered for screening by 12%. The implications of these findings are further discussed in the context of the HTS screening set and combinatorial library design as well as compound acquisition.

Drug Design↗
PubMed2004

Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results.

We have previously shown that a machine learning technique can improve the enrichment of high-throughput docking (HTD) results. In the previous cases studied, however, the application of a naive Bayes classifier failed to improve enrichment for instances where HTD alone was unable to generate an acceptable enrichment. We present here a protocol to rescue poor docking results a priori using a combination of rank-by-median consensus scoring and naive Bayesian categorization.

Algorithms↗