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Results for “high throughput”

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At least 883 records · Page 49Linked to original sources
PubMed2004

The use of precision glass syringes and a noncontact microsolenoid dispenser for the production of high-throughput low-density arrays.

The advantages of using nondisposable precision glass syringes in automated high-throughput microdispensers and a single-channel noncontact microsolenoid dispenser in creating highly uniform and reproducible protein, nucleic acid, and organic compound array filters, slides, and plates are described. Using a HydraPlus-One system, protein solutions of up to 100 mg/mL (in 100 nL) can be spotted onto slides and plates at a speed of 0.6 s per spot. Using the Hydra microdispenser and Tango liquid handling system, as little as 100 nL of polymerase chain reaction (PCR)-amplified human cancer-related genes, housekeeping genes, and protein solutions can be spotted onto nylon membranes, coated slides, or plates. Using these microdispensers equipped with syringes, up to 6144 uniform and reproducible spots per membrane and up to 1000 spots per slide, with a precision variation of less than 10%, were printed at a speed of as fast as 2.5 min per membrane.

Actins↗
PubMed2005

The discovery of novel protein kinase inhibitors by using fragment-based high-throughput x-ray crystallography.

This article describes the application of a high-throughput X-ray crystallographic fragment-based screening methodology to identify low-molecular-weight leads for structure-based optimisation into protein kinase inhibitors. The identification of two novel p38alpha MAP kinase inhibitors (with IC50=65 and 150 nM) starting from low-molecular-weight fragments is described.

Crystallography, X-Ray↗
PubMed2002

Multiple sprayer system for high-throughput electrospray ionization mass spectrometry.

A multiple sprayer electrospray ion source for high-throughput analysis is described. The ion source is comprised of multiple electrospray capillaries, each with an ion lens located near the tip. The electric potentials applied to the ion lenses are used to control the sprayers. The use of ion lenses eliminates the need for mechanical blocking devices to selectively enable or disable the sprayers, and results in a less expensive and more reliable set-up. Sprayers can be enabled or disabled within approximately 50-250 ms when the lens potentials are controlled manually. For simultaneous operation of multiple electrospray capillaries, it is advantageous to orient the capillaries so that the spray from each passes directly in front of the entrance aperture of the mass spectrometer.

Journal Article↗
PubMed2000

Quantitative, high-throughput cell-based assays for inhibitors of trkA receptor.

Two quantitative, high-throughput cell-based assays for evaluating inhibitors of NGF-stimulated trkA phosphorylation in trkA-transfected NIH3T3 cells have been established. Both assays involve capture of the trkA receptor from cell lysates in microtiter plates coated with an anti-trk antibody. The amount of trkA phosphorylation is then measured using either an anti-phosphotyrosine antibody with a colorimetric readout or a lanthanide (europium)-labeled anti-phosphotyrosine antibody with a fluorometric detection. The two assay formats exhibited at least a fivefold increase in phosphorylated trkA signal in trkA-transfected cells compared to vector control. Inhibition plots generated for trkA kinase inhibitors using the two detection systems yielded comparable IC(50) values. Overall, the two assays represent a marked improvement over the standard gel-based/western blot method in terms of throughput, quantitation, and amenability to automation.

3T3 Cells↗
PubMed2002

A comparative study of artificial membrane permeability assay for high throughput profiling of drug absorption potential.

Artificial membrane permeability measurement is a potentially high throughput and low cost alternative for in vitro assessment of drug absorption potential. It will be an ideal screening/profiling tool in the lead generation program of drug discovery research if it is proven to be generally applicable for classifying drug absorption potential and is advantageous over other in vitro or in silico methods. This study provides an in-depth evaluation of the method in close comparison to Caco-2, LogD, LogP, polar surface area (PSA), and quantitative structure-property relationship (QSPR) predictions using a large and diverse compound set. It showed that the accuracy of using artificial membrane permeability in assessing drug absorption is comparable to Caco-2, but significantly better than LogP, LogD, PSA, and QSPR predictions. This study also explored the artificial membrane composition by adopting a hydrophilic filter membrane for artificial membrane (lecithin-dodecane) support. The use of hydrophilic filter membrane increased the rate of permeation significantly and reduced the transport time to 2 h or less as compared with over 10 h when a hydrophobic filter membrane is used.

Caco-2 Cells↗
PubMed2003

A high-throughput screening system for genes extending life-span.

We developed a high-throughput functional genomic screening system that allows identification of genes prolonging life-span in the baker's yeast Saccharomyces cerevisiae. The method is based on isolating yeast mother cells with extended number of cell divisions as indicated by the increased number of bud scars on their surface. Fluorescently labelled Wheat Germ Agglutinin was used for specific staining of chitin, a major component of bud scars. Screening of a human HepG2 cDNA expression library in yeast resulted in the isolation of 12 yeast transformants with a potentially prolonged life-span. The transgene in one of the lines was identified as ferritin light chain (FTL) and studied in more detail. Yeast cells containing FTL showed an enhanced iron and H(2)O(2) resistance, a reduced cell death rate and an increased number of cell divisions. Overexpression of FTL in the nematode Caenorhabditis elegans resulted in a life-span increase of 8% confirming our yeast observations in a multicellular organism. Our data demonstrate that this method permits a fast screening of libraries for hunting genes involved in ageing processes.

Ferritins↗
PubMed2001

High-throughput assays on the chip based on metal nano-cluster resonance transducers.

High throughput transducers using metal cluster resonance technology are based on surface-enhancement of metal cluster light absorption. These devices can be used for detection of biorecognitive binding, as well as structural changes of nucleic acids, proteins or any other polymer. The optical property for the analytical application of metal cluster films is the so-called anomalous absorption. An absorbing film of clusters positioned 10--400 nm to a mirror surface reacts in a similar way to a reflection filter. At a certain distance of the absorbing layer to the mirror the reflected electromagnetic field has the same phase at the position of the absorbing cluster as the incident fields. This feedback mechanism strongly enhances the effective cluster absorption coefficient. The system is characterised by a narrow reflection minimum whose spectral position shifts sensitively with the interlayer thickness, because a given cluster-mirror distance and wavelength defines the optimum phase. Based on this principle a set of novel tools including biochips and micro arrays is presented, which enabled us to transduce binding, as well as changes of protein-, DNA- and polymer-conformation, quantitatively into an optical signal which can be observed directly as a colour change of a sensor-chip surface.

Electromagnetic Fields↗
PubMed2002

New approaches to high-throughput phasing.

Recent progress in macromolecular phasing, in part stimulated by the high-throughput structural biology initiatives, has made this crucial stage of the elucidation of crystal structures easier and more automatic. A quick soak in various salts leads to the rapid incorporation of the anomalously scattering ions, suitable for phasing by MAD (multiwavelength anomalous dispersion), SAD (single-wavelength anomalous dispersion) or MIR (multiple isomorphous replacement) methods. The availability of stable synchrotron beam lines equipped with elaborate hardware control and sophisticated data processing programs makes it possible to collect very accurate diffraction data and to solve structures from the very weak anomalous signal of such atoms as sulfur or phosphorus, inherently present in macromolecules. The current progress in phasing, coupled with the parallel advances in protein crystallization, diffraction data collection and so on, suggests that, in the near future, the process of macromolecular crystal structure elucidation may become fully automatic.

Algorithms↗
PubMed2006

High-throughput single-cell analysis for enzyme activity without cytolysis.

A novel high-throughput method without cytolysis for determination of enzyme activity inside single cells was developed by a combination of chemical cell perforation and an intracellular enzyme-catalyzed reaction. Peroxidase (PO) inside human neutrophils was chosen as the model system. Cells were perforated with digitonin to form micropores on the cell membrane. The perforated cells, with physiological buffer saline of pH 7.4 containing hydroquinone (H2Q) and H2O2, were continuously propelled by pressure through a capillary as the microsampler and microreactor. Small molecules H2Q and H2O2 could diffuse into the cell interior through the micropores on the cell membrane, and the large molecule PO remained in the cell interior. Intracellular PO converted H2Q into benzoquinone (BQ). BQ diffused out from the cell interior to the cell surface through the micropores and formed a BQ zone around the cell. The process proceeded in the capillary during cell movement. The BQ zones around every moving perforated cell were continuously delivered to the capillary outlet by hydraulic flow and detected. An average detection rate of >1 cell/min was obtained.

Catalysis↗
PubMed2005

High-throughput lipophilicity measurement with immobilized artificial membranes.

We report on a new, high-throughput assay designed to measure octanol/water partition coefficients in early drug discovery. The assay is carried out in 96-well microtiterplates and measures the diffusion of compounds between two aqueous compartments separated by a thin octanol liquid layer. Octanol/water partition coefficients are derived from the apparent permeability (P(a)) values using a calibration curve. The assay can measure partition coefficients within the range -2 to + 8; thus, a dynamic range of 10 log units can be covered in one single run. Unlike chromatographic methods, the technology is not restricted to neutral and weakly basic compounds, and, as no stationary phase is involved, the data can be strictly compared with values obtained from traditional methods such as shake-flask/HPLC or dual-phase potentiometric titration.

1-Octanol↗
PubMed2002

An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones.

We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing initiative, the method has been used and refined in our laboratory since September 2000. Amenable to large scale projects, we have used the method to generate >7 Mb of accurate sequence from 3695 candidate full-length cDNAs. Sequencing is accomplished through the insertion of Mu transposon into cDNAs, followed by sequencing reactions primed with Mu-specific sequencing primers. Transposon insertion reactions are not performed with individual cDNAs but rather on pools of up to 96 clones. This pooling strategy reduces the number of transposon insertion sequencing libraries that would otherwise be required, reducing the costs and enhancing the efficiency of the transposon library construction procedure. Sequences generated using transposon-specific sequencing primers are assembled to yield the full-length cDNA sequence, with sequence editing and other sequence finishing activities performed as required to resolve sequence ambiguities. Although analysis of the many thousands (22 785) of sequenced Mu transposon insertion events revealed a weak sequence preference for Mu insertion, we observed insertion of the Mu transposon into 1015 of the possible 1024 5mer candidate insertion sites.

Bacteriophage mu↗
PubMedDate not supplied

High-throughput purity estimation and characterisation of synthetic peptides by electrospray mass spectrometry.

High-throughput analysis for purity and molecular weight determination of synthetic peptides including characterisation of any peptidic byproducts arising from synthesis is described. The data from electrospray mass spectrometry are processed with an algorithm that calculates the contribution of the target peptide and each of the identifiable contaminants to the total ionizable material in a sample of synthetic peptide. All essential data are obtained by one instrumental technique in < 3 min per sample. The technique has distinct advantages in the rapid analysis of the many hundreds of peptides/peptidomimetics required in systematic quantitative structure-activity relationship and other investigations.

Algorithms↗
PubMed2000

Novel fluorescence sensing methods for high throughput screening.

We describe two new methods of fluorescence sensing for use in high throughput screening (HTS). Modulation sensing transforms analyte-dependent intensity changes into a change in the low-frequency modulation signal. Polarization sensing transforms an intensity change into a change in polarization. Both methods are internally calibrated by using a reference film immediately adjacent to the sample, which can be readily located on the HTS plate or on a nearby optical component and provides an intensity or polarization reference. Modulation sensing and polarization sensing were both shown useful for measurements of fluorophore concentrations, pH, or calcium concentrations in the wells of HTS plates. Sensing with a reference film provides the opportunity to internally reference HTS measurements without the need for additions to the sample. This approach can provide standardization for assays performed at different times.

Fluorescence Polarization↗
PubMed2001

Development of a high throughput screening assay for inhibitors of fibroblast growth factor-receptor-heparin interactions.

High throughput screening (HTS) of large compound libraries for inhibitors of growth factors raises the requirement for simple yet reliable assays. Fibroblast growth factors (FGFs) play a pivotal role in the multistep pathway of malignant transformation, tumor progression, metastasis, and angiogenesis. FGF-2 (basic FGF) requires a cooperative interaction with heparin or heparan sulfate proteoglycans in order to form functional growth factor-receptor complexes that are essential for receptor binding and activation. We have developed a simple screening system, devised to identify molecules that modulate heparin-FGF-receptor interactions. The system is composed of a heparin matrix, FGF-2, and a FGF receptor-1 protein engineered by genetically fusing the extracellular domain of FGF receptor-1 to alkaline phosphatase (FRAP). The screen is conducted using 96-well plates to which heparin has been covalently attached. FGF-2 is then bound to the plates through heparin-FGF interactions, followed by the addition of FRAP and compounds to be screened for modulation of heparin-FGF, receptor-heparin, and receptor-FGF interactions. The endpoint of the assay is measured enzymatically using the alkaline phosphatase (AP)-catalyzed formation of a chromogenic product, which is directly proportional to the amount of FRAP present on the plates as a heparin-FGF-FRAP ternary complex. Reduced AP values relative to control, as measured by spectrophotometry, indicate inhibition of the formation of an active FGF-receptor-heparin complex. The simple and versatile nature of the assay makes it an attractive HTS system. The screen has identified several potent inhibitors of FGF-2 receptor binding and activation. Furthermore, secondary screening of the HTS-recognized compounds identified several compounds that have the capacity to block growth factor-mediated tumor progression and angiogenesis in vivo.

Animals↗
PubMed2002

Outlier mining in high throughput screening experiments.

A data mining procedure for the rapid scoring of high-throughput screening (HTS) compounds is presented. The method is particularly useful for monitoring the quality of HTS data and tracking outliers in automated pharmaceutical or agrochemical screening, thus providing more complete and thorough structure-activity relationship (SAR) information. The method is based on the utilization of the assumed relationship between the structure of the screened compounds and the biological activity on a given screen expressed on a binary scale. By means of a data mining method, a SAR description of the data is developed that assigns probabilities of being a hit to each compound of the screen. Then, an inconsistency score expressing the degree of deviation between the adequacy of the SAR description and the actual biological activity is computed. The inconsistency score enables the identification of potential outliers that can be primed for validation experiments. The approach is particularly useful for detecting false-negative outliers and for identifying SAR-compliant hit/nonhit borderline compounds, both of which are classes of compounds that can contribute substantially to the development and understanding of robust SARs. In a first implementation of the method, one- and two-dimensional descriptors are used for encoding molecular structure information and logistic regression for calculating hits/nonhits probability scores. The approach was validated on three data sets, the first one from a publicly available screening data set and the second and third from in-house HTS screening campaigns. Because of its simplicity, robustness, and accuracy, the procedure is suitable for automation.

Algorithms↗
PubMed2004

A strategy for discovery of novel broad-spectrum antibacterials using a high-throughput Streptococcus pneumoniae transcription/translation screen.

The authors report the development of a high-throughput screen for inhibitors of Streptococcus pneumoniae transcription and translation (TT) using a luciferase reporter, and the secondary assays used to determine the biochemical spectrum of activity and bacterial specificity. More than 220,000 compounds were screened in mixtures of 10 compounds per well, with 10,000 picks selected for further study. False-positive hits from inhibition of luciferase activity were an extremely common artifact. After filtering luciferase inhibitors and several known classes of antibiotics, approximately 50 hits remained. These compounds were examined for their ability to inhibit Escherichia coli TT, uncoupled S. pneumoniae translation or transcription, rabbit reticulocyte translation, and in vitro toxicity in human and bacterial cells. One of these compounds had the desired profile of broad-spectrum biochemical activity in bacteria and selectivity versus mammalian biochemical and whole-cell assays.

Anti-Bacterial Agents↗
PubMed2005

Evaluating the high-throughput screening computations.

The judges evaluated the submissions for the McMaster University High-Throughput Data-Mining and Docking Competition based on 3 criteria: identification of active compounds, percent enrichment, and overview of the competition. Using these metrics, 4 of the participating groups found meaningful enrichment, and 3 groups made perceptive comments about the general nature of the competition.

Computational Biology↗