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Results for “high throughput”

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At least 775 records · Page 43Linked to original sources
PubMed2006

High-throughput isolation of ultra-pure plasmid DNA by a robotic system.

BACKGROUND: With the availability of complete genomes, a systematic inventory of cellular processes becomes achievable. This requires assessing the function of all individual genes. Transfection of plasmid DNA into cell culture cells is an essential technique for this aim as it allows functional overexpression or downregulation of genes. While many robotic systems isolate plasmids for sequencing purposes, for more demanding applications such as transfections there is a shortage of robots for the high-throughput isolation of plasmid DNA. RESULTS: Here we describe a custom-made, automated device, which uses a special protocol to isolate plasmid DNAs with a purity sufficient for efficient transfections into mammalian cells. Approximately 1,600 ultra pure plasmids can be isolated in a 96-well plate format within 12 hours. As a unique feature the robot comprises the integration of a centrifuge instead of expensive columns, the use of a custom-made pipetting head with a movable gripper, especially designed shaking platforms and an acetone wash facility. CONCLUSION: Using this robot we demonstrate how centrifugation steps with multiple precipitations, most notably through a precipitation step of SDS in isopropanol, lead to high purity plasmid DNA and make possible high-throughput transfections into mammalian cells for functional gene annotations.

Chemical Fractionation↗
PubMed2004

Use of high-throughput protein array for profiling of differentially expressed proteins in normal and malignant breast tissue.

cDNA arrays provide a powerful tool to identify gene expression pattern that are potentially associated with tumor invasion and metastasis. However, genes work at the protein level and, since the transcriptional activity of a gene does not necessarily reflect cellular protein expression, the identification and quantification of proteins is essential for the understanding of molecular events leading to malignant transformation. We have therefore employed a high-throughput protein microarray system which contains 378 well-characterized monoclonal antibodies in order to compare the gene expression pattern of malignant and adjacent normal breast tissue in a patient with primary breast cancer. Using this technique, we have identified a number of proteins that show increased expression levels in malignant breast tissues such as casein kinase Ie, p53, annexin XI, CDC25C, eIF-4E and MAP kinase 7. The expression of other proteins, such as the multifunctional regulator 14-3-3e was found to be decreased in malignant breast tissue, whereas the majority of proteins remained unchanged when compared to the corresponding non-malignant samples. The protein expression pattern was confirmed by immunohistochemistry, in which antibodies against 8 representative proteins known to be involved in carcinogenesis were employed in paraffin-embedded normal and malignant tissue sections deriving from the same patient. In each case, the results obtained by IHC matched the data obtained by antibody microarray system. Taken together, we have described for the first time a tumor cell specificity protein expression pattern by use of a novel commercially available antibody microarray system. We have thus demonstrated the feasibility of high-throughput protein arrays in the proteomic analysis of human breast tissue. We hypothesize that the use of protein arrays will not only increase our understanding of the molecular events, but could prove useful in evaluating prognosis and in determining optimal antineoplastic therapy.

Antibodies, Monoclonal↗
PubMed2004

Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing.

BACKGROUND: Mass spectrometry based proteomics result in huge amounts of data that has to be processed in real time in order to efficiently feed identification algorithms and to easily integrate in automated environments. We present wiff2dta, a tool created to convert MS/MS data obtained using Applied Biosystem's QStar and QTrap 2000 and 4000 series. RESULTS: Comparing the performance of wiff2dta with the standard tools, we find wiff2dta being the fastest solution for extracting spectrum data from ABIs raw file format. wiff2dta is at least 10% faster than the standard tools. It is also capable of batch processing and can be easily integrated in high throughput environments. The program is freely available via http://www.protein-ms.de, http://sourceforge.net/projects/protms/ and is also available from Applied Biosystems. CONCLUSIONS: wiff2dta offers the possibility to run as stand-alone application or within a batch process as command-line tool integrated in automation and high-throughput environments. It is more efficient than the state-of-the-art tools provided.

Automation↗
PubMed2006

High throughput solubility measurement with automated polarized light microscopy analysis.

As a high throughput solubility assay, the solution-precipitation method using a dimethylsulfoxide (DMSO) sample stock solution (DMSO-SP) has been widely used in drug discovery. However, the solid form of the precipitant has not been investigated. In this study, we investigated the experimental conditions of the DMSO-SP, focusing on the solid form of the precipitant. The final concentration of DMSO was 1% (v/v). The precipitant of more than a half of the model compounds was observed as crystalline by polarized light microscopy analysis. When the incubation time was 20 h and the precipitant was crystalline, the DMSO-SP solubility was similar to the solubility from a powder material (PWD). However, when the incubation time was 10 min and/or the precipitant was not crystalline, the DMSO-SP solubility was higher than the PWD solubility. These results suggested that the information regarding the solid form of the precipitant is important in interpreting the solubility data. In addition, we developed an automated birefringence diagnose system for drug discovery usage.

1-Octanol↗
PubMed2001

Uncovering biases in high throughput screens of G-protein coupled receptors.

The ability of high throughput membrane binding assays to detect ligands for G-protein coupled receptors was examined using mathematical models. Membrane assay models were developed using the extended ternary complex model (Samama et al., 1993) as a basis. Ligand binding to whole cells was modeled by adding a G-protein activation step. Results show that inverse agonists bind more slowly and with a lower affinity to receptors in the membrane binding assay than to receptors in whole cells, causing the membrane assay to miss pharmaceutically important inverse agonists. Assay modifications to allow detection of inverse agonists are discussed. Finally, kinetic binding data are shown to provide information about ligand efficacy. This work demonstrates the utility of mathematical modeling in detecting biases in drug-screening assay, and also in suggesting techniques to correct those biases.

Animals↗
PubMed1999

Detection of polymorphism in the RING3 gene by high-throughput fluorescent SSCP analysis.

We describe the use of a high-throughput, fluorescent, polymorphism-detection system, based on single-strand conformation polymorphism to screen for polymorphism in the RING3 gene. This is the first extensive mutation screen of this major histocompatibility complex-linked gene, and the entire coding region and intron-exon junctions were examined by multiplexing over 3000 polymerase chain reaction products. These techniques should be applicable for analysis of variation in other human genes. Investigation of DNA from acute lymphoblastic leukemia (ALL) and chronic myeloid leukemia (CML) patients, as well as healthy individuals revealed low levels of polymorphism across the RING3 gene. Comparison of the distribution of genotypes at each polymorphic site between patients and healthy individuals revealed a single site which significantly deviates from Hardy-Weinberg proportions.

Fluorescent Dyes↗
PubMed2005

High throughput P450 inhibition screens in early drug discovery.

This review of high throughput (HT) P450 inhibition technologies and their impact on early drug discovery finds the field at a mature stage. The relationship between P450 inhibition and drug-drug interactions is well understood. A wide variety of P450 inhibition detection technologies are readily available off-the-shelf, but what seems still to be missing is a general agreement on how much weight one should give to the various types of early discovery HT P450 inhibition data. Method-dependent potency differences are a cause of concern, and to resolve this issue the authors advocate calibration of the HT methods with a large set of marketed drugs.

Calibration↗
PubMed2002

Isotopically chiral probes for in situ high-throughput asymmetric reaction analysis.

In this work, we disclose a high-throughput screening assay for in situ analysis of enantioselection. The assay makes use of enantioenriched probe substrates that are isotopically chiral by virtue of a 13C isotope label. Upon catalytic asymmetric transformation, the carbon labels in the pseudoenantiomeric reaction products are in alternate diastereotopic environments and therefore lead to unique resonances. Simple integration allows for calculation of conversion and enantioselection.

Catalysis↗
PubMed2004

History, evolution, and trends in compound management for high throughput screening.

Growth in compound library size with increasing levels of high throughput screening has resulted in the complementary development of automated hardware and software systems for compound management. The history of this technology from its emergence in the early 1990s, its current status, and future trends are all described. The perspective is primarily a personal one, based on the author's involvement with compound management from its outset to the present day.

Agrochemicals↗
PubMedDate not supplied

Meeting report: high-throughput technologies for in vivo imaging agents.

Combinatorial chemistry and high-throughput screening have become standard tools for discovering new drug candidates with suitable pharmacological properties. Now, those same technologies are starting to be applied to the problem of discovering novel in vivo imaging agents. Important differences in the biological and pharmacological properties needed for imaging agents, compared to those for a therapeutic agent, require new screening methods that emphasize those characteristics, such as optimized residence time and tissue specificity, that make for a good imaging agent candidate.

Animals↗
PubMed1999

Single Molecule Detection Technologies in Miniaturized High Throughput Screening: Fluorescence Correlation Spectroscopy.

Fluorescence assay technologies used for miniaturized high throughput screening are broadly divided into two classes. Macroscopic fluorescence techniques (encompassing conventional fluorescence intensity, anisotropy [also often referred to as fluorescence polarization] and energy transfer) monitor the assay volume- and time-averaged fluorescence output from the ensemble of emitting fluorophores. In contrast, single-molecule detection (SMD) techniques and related approaches, such as fluorescence correlation spectroscopy (FCS), stochastically sample the fluorescence properties of individual constituent molecules and only then average many such detection events to define the properties of the assay system as a whole. Analysis of single molecular events is accomplished using confocal optics with an illumination/detection volume of approximately 1 fl (10(-15) L) such that the signal is insensitive to miniaturization of HTS assays to 1 µl or below. In this report we demonstrate the general applicability of one SMD technique (FCS) to assay configuration for target classes typically encountered in HTS and confirm the equivalence of the rate/equilibrium constants determined by FCS and by macroscopic techniques. Advantages and limitations of the current FCS technology, as applied here, and potential solutions, particularly involving alternative SMD detection techniques, are also discussed.

Journal Article↗
PubMed2005

Canonical Wnt signaling: high-throughput RNAi widens the path.

The canonical Wnt signaling pathway is highly conserved in evolution, widely used throughout animal development, and frequently hyperactive in cancer. Although Wnt signaling has been the subject of extensive genetic analysis in the past, some 200 genes have now been identified as candidate modulators of this pathway by a recent study using high-throughput RNAi screening.

Animals↗
PubMed2000

A neural network based virtual high throughput screening test for the prediction of CNS activity.

A virtual high throughput screening test to identify potentially CNS-active drugs has been developed. Discrimination was based on the knowledge available in databases containing CNS-active (Cipsline from Prous Science) and inactive compounds (Chemical Directory from Sigma-Aldrich). Molecular structures were represented using 2D Unit y fingerprints and a feedforward neural network was trained to classify molecules regarding their CNS activity. The parameterized network was validated by reclassification of the training set elements, by the classification of a test set preselected from the Prous database, and also by the prediction of activity for known CNS drugs not used in the training set but available in the Medchem database (Daylight). These tests revealed that our neural net recognized at least 89% of CNS-active compounds and would be suitable for use in our virtual screening protocol.

Artificial Intelligence↗
PubMed2000

Screening procedures for simultaneous detection of several drug classes used for high throughput toxicological analyses and doping control. A review.

This paper reviews high throughput screening procedures for the simultaneous detection of several drug classes relevant to clinical and forensic toxicology or doping control in urine or blood using gas chromatography-mass spectrometry (GC-MS), liquid chromatography coupled with a diode-array detector (LC-DAD) or mass spectrometry (LC-MS). Basic information describing these systematic toxicological analysis (STA) procedures such as the analytes, the biosample, work-up, separation column, mobile phase or separation buffer, detection mode and detection limits are summarized in tables arranged according to the analytical method. Examples of typical applications are presented in 2 figures. Analysis of alternative matrices, like sweat, saliva, nails or hair, was not reviewed.

Doping in Sports↗
PubMed2001

Introduction of the high throughput screening system.

In this article, we introduce the system of high throughput screening (HTS). Its role in new drug study and current development is described. The relationship between research achievements of genome study and new type screening model of new drugs is emphasized. The personal opinions of current problems about HIS study in China are raised.

Animals↗
PubMed2006

Label-free high-throughput functional lytic assays.

Refractive index-sensitive resonant waveguide grating biosensors are used to assay the label-free enzymatic degradation of biomolecules. These assays provide a robust means of screening for functional lytic modulators. The biomolecular substrates in this study were covalently immobilized through amine groups. Using the Corning Epic System, the digestion signatures for multiple protein substrates on the biosensors are measured. Label-free digestion profiles for these proteins were substrate specific. Similarly, the authors find that the label-free digestion is protease specific. Enzyme-substrate pairs were used to evaluate high- throughput biosensors as tools for screening functional modulators. The lytic inhibitor properties for several proteases and dextranase are determined. The authors find that the IC50 values for the protease inhibitors agree with the reported values for several known inhibitors. The Z' values, using biosensor-based functional lytic screens, were routinely greater than 0.5, making this label-free application feasible for high-throughput screening.

Animals↗
PubMed1999

A high throughput system for the evaluation of protein kinase C inhibitors based on Elk1 transcriptional activation in human astrocytoma cells.

Protein kinase C (PKC) designates a family of kinases that regulate many essential functions including cell growth and differentiation. The tight regulation of PKC activity is crucial for maintaining normal cellular proliferation and excessive activity leads to abnormal or uncontrolled cell growth. Recent reports indicate that malignant glioma cell lines express 100 to 1000-fold higher PKC activity when compared to non-neoplastic astrocytes. This high activity correlates well with the proliferation of tumor cells in vitro. We recently reported on the anti-proliferative properties of selective PKC inhibitors on the growth of U-373MG human astrocytoma cell line, and their ability to block mitogen-activated protein (MAP) kinase pathway activated by substance P (SP) neuropeptide receptor signaling via a PKC-dependent mechanism. Therefore, inhibiting PKC activity by selective PKC inhibitors may present a promising approach for improving astroglial brain tumor therapy. For this purpose, we constructed a high throughput model cell system to evaluate the efficacy of PKC inhibitors. This system is based on the measurement of light production in U-373MG cells stably transfected with the luciferase reporter gene whose expression depends on the transcriptional activation of GAL4-Elk1 fusion protein by enzyme components of the MAP kinase pathway and the upstream activation of PKC (PKC activation-->MAP kinases-->GAL4-Elk1 phosphorylation-->luciferase expression-->luciferase activity). In brief, we have demonstrated that the PKC activator 12-O-tetradecanoyl phorbol 13-acetate (TPA)-induced luciferase activity in this cell system is mediated via the MAP kinase pathway and can be blocked in the presence of MEK1 selective inhibitors (PD 098059 or U0126). We also demonstrated that TPA-induced luciferase activity in U-373MG stable clones can be blocked by PKC inhibitors (CGP 41251, Go 6976, and GF 109203X) in a concentration dependent manner. In contrast, epidermal growth factor (EGF)-induced luciferase activity, which is independent of PKC activation (Ras-->Raf-1-->MEK1-->MAP kinases-->GAL4-Elk1 phosphorylation-->luciferase expression-->luciferase activity) can only be blocked using a selective EGF receptor inhibitor (AG 1478). In conclusion, we have constructed a model cell system for the high throughput screening and identification of PKC inhibitors potentially active against astrocytoma cells in culture.

Antineoplastic Agents↗