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At least 1,585 records · Page 88Linked to original sources
PubMed2003

Development of an intact cell reporter gene beta-lactamase assay for G protein-coupled receptors for high-throughput screening.

G protein-coupled receptors (GPCRs) are involved in a large variety of physiological disorders, and are thus important pharmaceutical drug targets. Here, we describe the development and characterization of a beta-lactamase reporter gene assay as a functional readout for the ligand-induced activation of the human bradykinin B1 receptor, expressed recombinantly in CHO cells. The beta-lactamase reporter gene assay provides high sensitivity due to the absence of endogenous beta-lactamase activity in mammalian cells. The cell-permeable fluorogenic substrate allows single-cell cloning of cells expressing functional BK1 receptors. Pharmacological characterization reveals comparable sensitivity and potency of known BK1 receptor agonists and antagonists between the beta-lactamase assay, competition-binding assay, and other direct measurements of second messengers. The beta-lactamase assay has been optimized for cell density, time of agonist stimulation, and DMSO sensitivity. This CHO-hBK1-beta-lactamase assay is well suited to automation and miniaturization required for high-throughput screening.

Animals↗
PubMed2004

Discovery of transdermal penetration enhancers by high-throughput screening.

Although transdermal drug delivery is more attractive than injection, it has not been applied to macromolecules because of low skin permeability. Here we describe particular mixtures of penetration enhancers that increase skin permeability to macromolecules (approximately 1-10 kDa) by up to approximately 100-fold without inducing skin irritation. The discovery of these mixtures was enabled by an experimental tool, in vitro skin impedance guided high-throughput (INSIGHT) screening, which is >100-fold more efficient than current tools. In vitro experiments demonstrated that the mixtures delivered macromolecular drugs, including heparin, leutinizing hormone releasing hormone (LHRH) and oligonucleotides, across the skin. In vivo experiments on hairless rats with leuprolide acetate confirmed the potency and safety of one such mixture, sodium laureth sulfate (SLA) and phenyl piperazine (PP). These studies show the feasibility of using penetration enhancers for systemic delivery of macromolecules from a transdermal patch.

Administration, Cutaneous↗
PubMed2006

High-throughput screening methodology for the directed evolution of glycosyltransferases.

Engineering of glycosyltransferases (GTs) with desired substrate specificity for the synthesis of new oligosaccharides holds great potential for the development of the field of glycobiology. However, engineering of GTs by directed evolution methodologies is hampered by the lack of efficient screening systems for sugar-transfer activity. We report here the development of a new fluorescence-based high-throughput screening (HTS) methodology for the directed evolution of sialyltransferases (STs). Using this methodology, we detected the formation of sialosides in intact Escherichia coli cells by selectively trapping the fluorescently labeled transfer products in the cell and analyzing and sorting the resulting cell population using a fluorescence-activated cell sorter (FACS). We screened a library of >10(6) ST mutants using this methodology and found a variant with up to 400-fold higher catalytic efficiency for transfer to a variety of fluorescently labeled acceptor sugars, including a thiosugar, yielding a metabolically stable product.

Amino Acid Sequence↗
PubMed2004

High throughput immuno-screening of cDNA expression libraries produced by in vitro recombination; exploring the Plasmodium falciparum proteome.

Improved Plasmodium falciparum cDNA expression libraries were constructed by combining mRNA oligo-capping with in vitro recombination and directional cloning of cDNA inserts into a plasmid vector that expresses sequences as thioredoxin fusion proteins. A novel procedure has also been developed for the rapid identification of seropositive clones on high-density filters, using direct labelling of P. falciparum immune immunoglobulin with fluorescein isothiocynate (FITC). This approach combines the advantages of recombination-assisted cDNA cloning with high throughput, non-radioactive serological screening of expression libraries. Production of replicate colony matrices allows the identification of antigens recognised by different pools with different specificities from residents of a malaria endemic region. Analyses of DNA sequences derived from sero-reactive colonies indicate that this is an effective method for producing recombinant proteins that react with antibodies from malaria-exposed individuals. This approach permits the systematic construction of a database of antigenic proteins recognised by sera from malaria-exposed individuals.

Animals↗
PubMed2000

High-throughput single-molecule DNA screening based on electrophoresis.

In electrophoresis, the migration velocity is used for sizing DNA and proteins or for distinguishing molecules based on charge and hydrodynamic radius. Many protein and DNA assays relevant to disease diagnosis are based on such separations. However, standard protocols are not only slow (minutes to hours) but also insensitive (many molecules in a detectable band). We successfully demonstrated a high-throughput imaging approach that allows determination of the individual electrophoretic mobilities of many molecules at a time. Each measurement only requires a few milliseconds to complete. This opens up the possibility of screening single copies of DNA or proteins within single biological cells for disease markers without performing polymerase chain reaction or other biological amplification. The purpose is not to separate the DNA molecules but to identify each one on the basis of the measured electrophoretic mobility. We developed three different procedures to measure the individual molecular mobilities. The results correlate well with capillary electrophoresis (CE) experiments for the same samples (2-49 kb dsDNA) under identical separation conditions. The implication is that any electrophoresis protocols from slab gels to CE should be adaptable to single-molecule screening for disease diagnosis.

Buffers↗
PubMed2006

High-throughput sequence determination of cyclic peptide library members by partial Edman degradation/mass spectrometry.

Cyclic peptides provide attractive lead compounds for drug discovery and excellent molecular probes in biomedical research. Large combinatorial libraries of cyclic peptides can now be routinely synthesized by the split-and-pool method and screened against biological targets. However, post-screening sequence determination of hit peptides has been problematic. In this report, a high-throughput method for the sequence determination of cyclic peptide library members has been developed. TentaGel microbeads (90 mum) were spatially segregated into outer and inner layers; cyclic peptides were displayed on the bead surface, whereas the inner core of each bead contained the corresponding linear peptide as the encoding sequence. After screening of the cyclic peptide library against a macromolecular target, the identity of hit peptides was determined by sequencing the linear encoding peptides inside the bead using a partial Edman degradation/mass spectrometry method. On-bead screening of an octapeptide library (theoretical diversity of 160 000) identified cyclic peptides that bind to streptavidin. A 400-member library of tyrocidine A analogues was synthesized on TentaGel macrobeads and solution-phase screening of the library directly against bacterial cells identified a tyrocidine analogue of improved antibacterial activity. Our results demonstrate that the new method for cyclic peptide sequence determination is reliable, operationally simple, rapid, and inexpensive and should greatly expand the utility of cyclic peptides in biomedical research.

Anti-Infective Agents↗
PubMed2003

Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking.

To assess the potential of protein kinase CK2 as a target for developing new antitumor agents, we have undertaken a search for inhibitors of this enzyme. As part of this effort, we report here the discovery of the potent and selective CK2 inhibitor (5-oxo-5,6-dihydroindolo[1,2-a]quinazolin-7-yl)acetic acid. We identified this inhibitor of a novel structural type by high-throughput docking of our corporate compound collection in the ATP binding site of a homology model of human CK2, using an appropriate protocol. The synthesis of the inhibitor as well as that of related analogues whose CK2 inhibitory activities give support to the binding mode proposed by the docking program is described. The results obtained suggest that virtual screening of a 3D database by molecular docking is a useful approach for lead finding provided that adapted postdocking filtering and reranking procedures are applied to the primary hit list.

Acetates↗
PubMed2005

High-throughput site-directed mutagenesis using oligonucleotides synthesized on DNA chips.

Site-directed mutagenesis has greatly helped researchers both to understand the precise role of specific residues in coding sequences and to generate variants of proteins that have acquired new characteristics. Today's demands for more complete functional cartographies of proteins and advances in selection and screening technologies require that site-directed mutagenesis be adapted for high-throughput applications. We describe here the first generation of a library of single and multiple site-directed mutants using a mixture of oligonucleotides synthesized on DNA chips. We have used the human interleukin 15 (IL15) gene as a model, of which 37 codons were simultaneously targeted for substitution by any of eight possible codons. Ninety-six clones were sequenced, exhibiting a broad spectrum of targeted substitutions over the whole gene length with no unwanted mutations. Libraries produced using such pools of oligonucleotides open new perspectives to direct the evolution of proteins in vitro, by enabling the simple, rapid, and cost-effective generation of large tailor-made genetic diversities from any gene.

Gene Library↗
PubMed2000

High throughput analysis of gene expression in the human brain.

The human brain is thought to have the greatest complexity of gene expression of any region of the body, reflecting the diverse functions of neurons and glia. Studies of gene expression in the human brain may yield fundamental information about the phenotype of brain cells in different stages of development, in different brain regions, and in different physiological and pathological states. As the human genome project nears completion, several technological advances allow the analysis of thousands of expressed genes in a small brain sample. This review describes available sources of human brain material, and several high throughput techniques used to measure the expression of thousands of genes. These techniques include expressed sequence tag (EST) sequencing of cDNA libraries; differential display; subtractive hybridization; serial analysis of gene expression (SAGE); and the emerging technology of high density DNA microarrays. Measurement of gene expression with microarrays and other technologies has potential applications in the study of human brain diseases, including cognitive disorders for which animal models are typically not available. Gene expression measurements may be used to identify genes that are abnormally regulated as a secondary consequence of a disease state, or to identify the response of brain cells to pharmacological treatments.

Animals↗
PubMed2007

Application of phenylboronic acid modified hydrogel affinity chips for high-throughput mass spectrometric analysis of glycated proteins.

The complexity of the human plasma proteome is greatly increased by post-translational modifications. Besides physiological modifications, pathological conditions such as diabetes are responsible for adding to this complexity by producing advanced glycation endproducts (AGEs). When searching for specific biomarkers it is a prerequisite to reduce this complexity prior to analysis. To do this, agarose hydrogel was used to create a high-capacity affinity layer on the modified aluminum surface of MALDI (matrix-assisted laser desorption/ionization) targets. 3-Aminophenylboronic acid was immobilized via cyanogen bromide activation as a ligand for affinity sorption of glycated proteins, followed by their direct detection by MALDI. High protein capacity of prepared MALDI chips, efficient separation and low non-specific protein binding were demonstrated. The results show that phenylboronic acid modified hydrogels are very suitable for creating affinity surfaces for the high-throughput analysis of AGEs.

Aluminum↗
PubMed1997

A high-throughput STAT binding assay using fluorescence polarization.

STAT (signal transducers and activators of transcription) is a class of transcription factors that are activated upon cytokine or growth factor binding to cell surface receptors. Activated STAT proteins dimerize, translocate into the nucleus, and activate transcription, leading to various immune responses. The inhibition of STAT binding to cell receptors might provide a means to modulate these immune responses. We developed a high-throughput biochemical assay to measure the interaction between an interferon-gamma receptor-derived phosphotyrosine-containing peptide and STAT1, using fluorescence polarization as the detection method. This assay can be used to screen for small molecules capable of disrupting receptor-STAT interactions.

Binding, Competitive↗
PubMed2001

High-throughput reactor for simulating the flame photometric detector.

Quenching of luminescing species by co-eluting hydrocarbons has been widely reported in the flame photometric detector (FPD). This paper describes a novel method of investigating the chemical behavior of both analyte and quencher molecules in the FPD. The method is designed to reproduce the FPD's behaviour on a large scale by using a custom-built reactor. The high-throughput reactor's multi-capillary burner, situated inside a glass housing, is well suited to approximate the low-temperature, fuel-rich conditions of the conventional FPD, and also allows the study of various other flame phenomena. Wide regions of gas composition can be accessed by both diffusion- and premixed-type flames, and products can be easily sampled. Effluent collection demonstrates that 2 to 82% of various organic compounds may survive passage through the diffusion flame and be recovered intact. The recovery of several (unchanged) model hydrocarbons was found to decrease with increasing carbon number. Hetero-atoms such as sulfur, nitrogen, or oxygen greatly decrease the recovery of molecules relative to their pure hydrocarbon analogues. Compared to a diffusion flame, the recoveries of n-alkanes from a premixed flame are much lower and largely independent of carbon number or volatility.

Chromatography, Gas↗
PubMed2002

Progress in high throughput SNP genotyping methods.

Most current single nucleotide polymorphism (SNP) genotyping methods are still too slow and expensive for routine use in large association studies with hundreds or more SNPs in a large number of DNA samples. However, SNP genotyping technology is rapidly progressing with the emergence of novel, faster and cheaper methods as well as improvements in the existing methods. In this review, we focus on technologies aimed at high throughput uses, and discuss the technical advances made in this field in the last few years. The rapid progress in technology, in combination with the discovery of millions of SNPs and the development of the human haplotype map, may enable whole genome association studies to be initiated in the near future.

Animals↗
PubMed2006

High throughput assays for analyzing transcription factors.

Transcription factors are a group of proteins that modulate the expression of genes involved in many biological processes, such as cell growth and differentiation. Alterations in transcription factor function are associated with many human diseases, and therefore these proteins are attractive potential drug targets. A key issue in the development of such therapeutics is the generation of effective tools that can be used for high throughput discovery of the critical transcription factors involved in human diseases, and the measurement of their activities in a variety of disease or compound-treated samples. Here, a number of innovative arrays and 96-well format assays for profiling and measuring the activities of transcription factors will be discussed.

Biological Assay↗
PubMed2006

A high-throughput approach for associating MicroRNAs with their activity conditions.

Plant microRNAs (miRNAs) are short RNA sequences that bind to target mRNAs and change their expression levels by redirecting their stabilities and marking them for cleavage. In Arabidopsis thaliana, microRNAs have been shown to regulate development and are believed to impact expression both under various conditions, such as stress and stimuli, as well as in specific tissue types. We present a high throughput approach for associating between microRNAs and conditions in which they act, using novel statistical and algorithmic techniques. Our new tool, miRNAXpress, at first computes a (binary) matrix T denoting the potential targets of microRNAs. Then, using T and an additional predefined matrix X indicating expression of genes under various conditions, it produces a new matrix that predicts associations between microRNAs and the conditions in which they act. Thus, the program comprises two main modules that work in tandem to compute the desired output. The first is an efficient target prediction engine that predicts mRNA targets of query microRNAs by evaluating the optimal duplex that could be formed between the two: given a short query RNA, a long target RNA, and a predefined energy cut-off threshold, the program finds and reports all putative binding sites of the query RNA in the target RNA with hybridization energy bounded by the predefined threshold. The second module realizes an association operation that is computed by a method which relies on an efficient t-test to compute the associations. The calculation of the matrix of microRNAs and their potential targets is the computationally intensive part of the work done by miRNAXpress, and therefore an efficient algorithm for this portion facilitates the entire process. Thus, the target prediction engine is based on an efficient approximate hybridization search algorithm whose efficiency is the result of utilizing the sparsity of the search space without sacrificing the optimality of the results. The time complexity of this algorithm is almost linear in the size of a sparse set of locations where base-pairs are stacked at a height of three or more. Thus miRNAXpress is a novel tool for associating between microRNAs and the conditions in which they act. We employed it to conduct a study, using the plant Arabidopsis thaliana as our model organism. By applying miRNAXpress to 98 microRNAs and 380 conditions, some biologically interesting and statistically strong relations were discovered. For example, mir159C activity is possibly a factor in the misresponse of nph4 mutants to phototropic stimulations.

Arabidopsis↗
PubMed2002

A high-throughput screening procedure for identifying mice with aberrant taste and oromotor function.

Little is known about how specific genes influence taste function in mammals. One of the most promising ways to fill this void is to screen the progeny of chemically mutagenized (or genetically altered) mice for aberrant taste phenotypes and then identify the mutated gene(s) that is associated with each taste anomaly. To exploit this approach, a high-throughput and robust screening procedure is needed. We have attempted to meet this demand by developing an automated procedure that assesses taste responsiveness of individual mice to palatable and unpalatable taste stimuli. We focused on three taste stimuli (quinine hydrochloride, QHCl; sodium chloride, NaCl; and sucrose) and one mouse strain (C57BL/6). We used a commercially available gustometer system that both monitors the licking responses of mice and controls the presentation of each taste stimulus during successive 5 s trials. We describe a screening procedure that (after 2 days of simple training) can generate a concentration-response curve for NaCl or sucrose during a single 30 min test session, and for QHCl over three 30 min test sessions. A normative database based on the responses of 98 mice subjected to our screening procedure is also presented. We envision that investigators could use this normative database to assess taste function in the progeny of mutagenized (or genetically altered) mice. Any mouse that deviates significantly-e.g. three standard deviations (SD)-from the mean of the normative database would be flagged as having a potentially interesting mutation. We also developed an additional second screen for identifying mice with oromotor abnormalities. This latter screen is necessary because oromotor problems could lead to false positives or negatives in the screen for taste function, but is also useful for researchers interested in genes influencing oromotor circuitry. Throughout the development of the screening protocol, we sought to balance two conflicting demands: the need to maximize the screen's sensitivity and minimize its duration. This screen represents a significant improvement over the common two-bottle preference test because it assesses taste function more specifically and in a fraction of the time.

Animals↗
PubMed2003

A cell-based high-throughput screening system for detecting ecdysteroid agonists and antagonists in plant extracts and libraries of synthetic compounds.

Screening systems for ecdysteroid mimetic or antiecdysteroid substances in plant extracts or libraries of synthetic compounds are commonly based on the observation of morphological and/or growth responses in insect cell lines. Because these responses are slow and require careful monitoring, existing screening systems are considered limited regarding their applicability to analysis in high-throughput (HT) formats. Here we describe the generation of transformed silkmoth (Bombyx mori) cell lines that respond to the addition of ecdysone-like substances through the expression of the green fluorescent protein (GFP) and the appearance of green fluorescence. Because tests consist of three simple steps, i.e., 1) distribution of transformed cells in microtiter plates; 2) addition of compounds/extracts at different concentrations; and 3) quantification of fluorescence intensity by a fluorescence plate reader, they can be performed quickly and be easily adapted to a HT format. The generated reporter cell lines are used for the screening of extracts from available plant collections for the presence of compounds with ecdysone mimetic or antagonistic activities as well as for monitoring subsequent activity during enrichment and purification steps. The same cell lines are also used here for the determination of structure-activity relationships among available synthetic dibenzoylhydrazine derivatives. Finally, for the identified agonists, we show that their activity as determined by the cell-based screening assays parallels their bioactivity in growth inhibition and toxicity assays carried out on live insects.

Animals↗
PubMed1998

High-throughput assay for G2 checkpoint inhibitors and identification of the structurally novel compound isogranulatimide.

Treatment of cancer cells lacking p53 function with G2 checkpoint inhibitors sensitizes them to the toxic effects of DNA damage and has been proposed as a strategy for cancer therapy. However, few inhibitors are known, and they have been found serendipitously. We report the development of a G2 checkpoint inhibition assay that is suitable for high-throughput screening and its application to a screen of 1300 natural extracts. We present the isolation of a new G2 checkpoint inhibitor, the structurally novel compound isogranulatimide. In combination with gamma-irradiation, isogranulatimide selectively kills MCF-7 cells lacking p53 function.

Adenocarcinoma↗