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PubMed2006

Automated liquid handling and high-throughput preparation of polymerase chain reaction-amplified DNA for microarray fabrication.

Genome-wide studies of gene expression and transcription factor-binding sites using DNA microarrays are leading to new systems level insights. The massively parallel nature of microarrays presents technical challenges: fabricating high-quality microarrays at the front end and data analysis and interpretation downstream. A principal challenge in fabricating microarrays is preparation of the DNA samples. This is particularly the case for polymerase chain reaction-amplified DNA samples. The challenge is to scale up efficiently to high-throughput preparation of tens of thousands of DNA samples while ensuring a uniform high quality. This chapter outlines strategic considerations, including automated liquid handling and workflow development to maximize efficiency, and quality control (QC) measures to ensure uniform quality. The protocols are presented with commentary to illustrate their logic and specific techniques. These principles and techniques are extensible to other high-throughput molecular biological applications.

Animals↗
PubMed2002

In vitro high-throughput screening assay for modulators of transcription.

We developed a 96-well microtiter-plate high-throughput screening (HTS) assay for the detection of modulators of transcription. This HTS assay consists of three steps: (1) the in vitro transcription reaction; (2) modification and hybridization of RNA products; and (3) washing and quantification. During the first step, a DNA template containing the promoter of interest upstream of a cassette lacking guanosine residues in one of its strands (G-less cassette) is incubated with nuclear extract and the necessary cofactors/activators and substrates. During the second step, the in vitro synthesized transcripts are digested with RNase T1 and hybridized to two DNA oligonucleotides. One oligonucleotide is biotinylated for trapping of the RNA products to a streptavidin-coated plate, and the other is europium-labeled for detection by time-resolved fluorescence. We show that this assay is highly reproducible and robust, yielding results comparable to those obtained by standard methodologies employing radioactive nucleotide incorporation and gel electrophoresis while offering a very significant advantage in terms of throughput (>2000 assay points per operator per day). We demonstrate the usefulness of the assay for the discovery of small molecule inhibitors of transcription, and applications of this approach for the high-throughput discovery of transcriptional modulators are discussed.

Amanitins↗
PubMedDate not supplied

Development of field modulation in a split-field drift tube for high-throughput multidimensional separations.

A field modulation approach for high-throughput ion mobility/time-of-flight analyses of complex mixtures has been developed using a split-field drift tube. In this approach, complex mixtures of peptides, such as those that arise from tryptic digestion of protein mixtures, are separated by nanocolumn liquid chromatography, ionized by electrospray ionization, and analyzed by ion mobility/time-of-flight techniques. The split-field drift tube allows parent ions to be separated based on differences in their low-field mobilities through the first-field region before entering the second region. For increased throughput, the magnitude of the field in the second region can be modulated throughout an LC separation in order to favor transmission of different types of ions: parent ions at low fields; fragments from primarily [M+3H]3+ peptides at moderate fields; or, fragmentation of [M+3H]3+ and [M+2H]2+ species at higher fields. We demonstrate the approach with two examples: a mixture of tryptic peptides from digestion of hemoglobin; and a complex mixture of tryptic peptides from digestion of human plasma.

Blood Proteins↗
PubMed2003

Agrosuppression: a bioassay for the hypersensitive response suited to high-throughput screening.

We describe a novel method, agrosuppression, that addresses the need for an assay of the hypersensitive response (HR) in intact plants that is rapid and adapted to high-throughput functional screening of plant and pathogen genes. The agrosuppression assay is based on inoculation of intact plants with a mixture of Agrobacterium tumefaciens strains carrying (i) a binary plasmid with one or more candidate HR-inducing genes and (ii) a tumor-inducing (oncogenic) T-DNA. In the absence of HR induction, tumor formation is initiated, resulting in a typical crown gall phenotype. However, upon induction of the HR, tumor formation by the oncogenic T-DNA is suppressed, resulting in a phenotype that can be readily scored. We tested and optimized agrosuppression in Nicotiana benthamiana using the inf1 elicitin gene from the oomycete pathogen Phytophthora infestans, which specifically induces the HR in Nicotiana spp., and the gene-for-gene pair Avr9/Cf-9 from the fungal pathogen Cladosporium fulvum and Lycopersicon pimpinellifolium (currant tomato), respectively. Agrosuppression protocols that can be rapidly performed using simple mechanical wounding of petioles of intact N. benthamiana plants were developed and appeared particularly adapted to intensive high-throughput screening. This assay promises to greatly facilitate the cloning of novel plant R genes and pathogen Avr genes and to accelerate functional analyses and structure-function studies of these genes.

Agrobacterium tumefaciens↗
PubMed2001

Multilamellar liposomes and solid-supported lipid membranes (TRANSIL): screening of lipid-water partitioning toward a high-throughput scale.

PURPOSE: Lipid-water partitioning of 187 pharmaceuticals has been assessed with solid-supported lipid membranes (TRANSIL) in microwell plates and with multilamellar liposomes for a data comparison. The high-throughput potential of the new approach was evaluated. METHODS: Drugs were incubated at pH 7.4 with egg yolk lecithin membranes either on a solid support (TRANSIL beads) or in the form of multilamellar liposomes. Phase separation of lipid and water phase was achieved by ultracentrifugation in case of liposomes or by a short filtration step in case of solid-supported lipid membranes. RESULTS: Lipid-water partitioning data of both approaches correlate well without systematic deviations in the investigated lipophilicity range. The solid-supported lipid membrane approach provides high-precision data in an automated microwell-plate setup. The lipid composition of the solid-supported lipid membranes was varied to study the influence of membrane change on lipid-water partitioning. In addition, pH-dependent measurements have been performed with minimal experimental effort. CONCLUSIONS: Solid-supported lipid membranes represent a valuable tool to determine physiologically relevant lipid-water partitioning data of pharmaceuticals in an automated setup and is well suited for high-throughput data generation in lead optimization programs.

Chromatography, High Pressure Liquid↗
PubMed2006

High-throughput determination of quantitative structure-property relationships using a resonant multisensor system: solvent resistance of bisphenol a polycarbonate copolymers.

Polymers are important materials for sensor, microfluidic, and other demanding applications. High-throughput screening methodology has been applied for the evaluation of the solvent resistance of a family of polycarbonate copolymers prepared from the reaction of bisphenol A (BPA), hydroquinone (HQ), and resorcinol (RS) in different solvents of practical importance, such as chloroform, tetrahydrofuran (THF), and methyl ethyl ketone (MEK). We employed a 24-channel acoustic-wave sensor system that provided previously unavailable capabilities for parallel evaluation of polymer solvent resistance. This high-throughput polymer evaluation approach assisted in construction of detailed solvent-resistance maps of polycarbonate copolymers and in determination of quantitative structure-property relationships. The best absolute solvent resistance of all studied copolymers was achieved in MEK, followed by chloroform and THF. A D-optimal mixture design was employed to explore the relationship between the copolymer compositions and their solvent resistance. The applied special cubic model for each solvent took into account the primary mixture terms such as BPA, HQ, and RS; binary interaction terms such as BPA-HQ, BPA-RS, and HQ-RS; and a ternary interaction term BPA-HQ-RS. A combination of the normal distribution of the model residuals and the very high values of adjusted R2 (0.97-0.99) demonstrated a good quality of the model. At a HQ concentration of 40 mol %, the solvent resistance was the highest for all tested solvents, and different concentrations of BPA (40 and 60 mol %) and RS (0 and 20 mol %) did not affect the solvent resistance. Without HQ, solvent resistance was decreasing with an increase of RS and decrease of BPA. Overall, with an increase of HQ concentration from 0 to 40 mol %, the solvent resistance of BPA-HQ-RS copolymers was improved by up to 3 times in THF, by 21 times in chloroform, and by 32 times in MEK.

Journal Article↗
PubMed2003

Water-compatible molecularly imprinted polymers obtained via high-throughput synthesis and experimental design.

A technique allowing high-throughput synthesis and evaluation of molecularly imprinted polymer sorbents at a reduced scale (mini-MIPs) was developed and used for the optimization of MIPs for use in pure aqueous environments. The technique incorporated a 4-port liquid-handling robot for the rapid dispensing of monomers, templates, solvents and initiator into the reaction vessels of a 96-well plate. A library of 80 polymers, each ca. 50 mg, could thus be prepared in 24 h. The MIP rebinding capacity and selectivity could be rapidly assessed in the batch mode by quantifying nonbound fractions in parallel using a UV monochromator plate reader. This allowed a complete evaluation of the binding characteristics of an 80 polymer library in approximately 1 week. With the objective of optimizing a polymer imprinted with the local anaesthetic Bupivacaine for use in pure aqueous systems, a polymer library was prepared by varying the original poly(MAA-co-EDMA) MIP composition. The variable factors were the added amount of the hydrophilic comonomer, 2-hydroxyethyl methacrylate (HEMA), the cross-linking ratio, and the porogen. This optimization resulted in polymers showing high imprinting factors (IF = K(MIP)/K(NIP)) in water as a result, mainly, of reduced binding to the nonimprinted polymer. Normal scale batches of these materials showed strong retention of the template and low nonspecific binding when assessed as chromatographic stationary phases using pure phosphate buffer, pH 7.4, as mobile phase, by equilibrium batch rebinding experiments and as sorbents for extractions of the analyte from blood plasma samples.

Journal Article↗
PubMed2004

Techniques for high-throughput characterization of peptides, oligonucleotides and catalysis efficiency.

Combinatorial processes have been widely applied to many disciplines in chemistry and biology. The vast numbers of unique entities generated by combinatorial synthesis have led to the development of high-throughput methods for characterizing samples, to avoid bottlenecks created by the application of conventional, serial-based analytical techniques. In recent years, high-throughput and novel methods utilizing mass spectrometry, multiplexed capillary electrophoresis, various forms of optical detection, and even sound waves have been investigated for a variety of applications.

Catalysis↗
PubMed2003

Progress in liquid chromatography-mass spectrometry instrumentation and its impact on high-throughput screening.

In the past 10 years, liquid chromatography-mass spectrometry (LC-MS) has rapidly matured to become a very powerful and useful analytical tool that is widely applied in many areas of chemistry, pharmaceutical sciences and biochemistry. In this paper, recent instrumental developments in LC-MS-related interfacing, ionization and mass analysis are reviewed from the perspective of the application of LC-MS in high-throughput screening of combinatorial libraries and the related high-throughput quantitative bioanalysis in early drug-discovery studies, such as early adsorption, distribution, metabolism and excretion studies.

Chromatography, Liquid↗
PubMed2005

High performance liquid chromatography equipped with a cathodic detector and column-switching device as a high-throughput method for a phosphatase assay with p-nitrophenyl phosphate.

LC coupled to an electrochemical detector (LC-EC) operating in cathodic mode with a column-switching system realizes a high-throughput detection of p-nitrophenol (NP). The measurement-time for each NP sample was shortened to 20 s, and the successive analyses of 39 samples was completed within 13 min. In the present system, the limits of detection and quantification were 0.15 and 0.20 microM, respectively, and further, up to 25 microM, a linear calibration curve was afforded. Relative standard deviations for standard solutions of 0.20, 1.0, and 25 microM NP were 4.3, 2.0, and 1.1% (n = 5), respectively. Between-run precisions of the analysis of 5.0 and 25 microM NP over 6 days were 4.8 and 1.3%, respectively. A comparison with the commonly used Bessey-Lowry-Brock method indicates that the present LC-EC is useful for the high-throughput assay of acid and alkaline phosphatases in urine and blood samples with a p-nitrophenyl phosphate substrate.

Acid Phosphatase↗
PubMed1997

An automated high throughput filtration assay: application to polymerase inhibitor identification.

A high throughput filtration assay was developed and automated for screening compounds and natural product extracts using 96-well filterplates. The selection of a hydrophobic membrane and appropriate capture conditions enabled us to perform the enzymatic reaction, capture of products, vacuum filtration, and detection in a single filtration microplate, without any transfer step. The hydrophobic membrane has the advantage of preventing any loss of aqueous solution during the enzymatic reaction. The results are comparable with those obtained in a solid plate format followed by transferring the reaction mixture to a traditional hydrophilic filterplate. This assay is being used to screen for microbial RNA polymerase inhibitors as potential new drugs for treatment of emerging antibiotic-resistant bacterial and fungal infections. The filtration setup can be applied to a variety of assay systems.

Cytidine Triphosphate↗
PubMed2002

High-throughput protein characterization using mass spectrometric immunoassay.

A high-throughput mass spectrometric immunoassay system for the analysis of proteins directly from plasma is reported. A 96-well format robotic workstation was used to prepare antibody-derivatized affinity pipette tips for subsequent use in the extraction of specific proteins from plasma and deposition onto 96-well format matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) targets. Samples from multiple individuals were screened with regard to the plasma protein transthyretin (TTR), followed by analysis of the same plasma samples for the transthyretin-associated transport protein, retinol-binding protein (RBP). Analyses were able to detect the presence of posttranslationally modified TTR and RBP, as well as a mutation present in the TTR of one individual. Subsequent analyses of wild-type and mutated TTR using enzymatically active MALDI-TOF MS targets were able to identify the site and nature of the point mutation. The approach represents a rapid (approximately 100 samples/2 h, reagent preparation-to-data) and accurate means of characterizing specific proteins present in large numbers of individuals for proteomic and clinical/diagnostic purposes.

Antibody Affinity↗
PubMed2006

High throughput screening in drug discovery.

Drug discovery is a highly complex and multidisciplinary process which goal is to identify new antitumoral drugs. The screening attrition rate in the current drug discovery protocols suggests that one marketable drug emerges from approximately one million screened compounds. This leads to pressure to screen larger libraries in order to continue the pipeline and to the development of High Throughput Screening. HTS is only a name for specific developments in laboratory automation to collect a large amount of experimental data in a relatively short time. HTS can test hundreds of thousands of compounds per day, however, if fewer compounds could be tested without compromising the probability of success, the cost and time would be greatly reduced. To that end, new developments in large-scale cell biology and compound library design in silico have evolved to obtain data with higher predictability of clinical efficacy.

Animals↗
PubMed2005

A high-throughput screening for phosphatases using specific substrates.

A high-throughput screening was developed for the detection of phosphatase activity in bacterial colonies. Unlike other methods, the current procedure can be applied to any phosphatase because it uses physiological substrates and detects the compelled product of all phosphatase reactions, that is, orthophosphate. In this method, substrates diffuse from a filter paper across a nitrocellulose membrane to bacterial colonies situated on the opposite face, and then reaction products flow back to the paper. Finally, a colorimetric reagent discloses the presence of orthophosphate in the filter paper. We validated the performance of this assay with several substrates and experimental conditions and with different phosphatases, including a library of randomly mutagenized rapeseed chloroplast fructose-1,6-bisphosphatase. This procedure could be extended to other enzymatic activities provided that an appropriate detection of reaction products is available.

Alkaline Phosphatase↗
PubMed2006

A cell-based luminescence assay is effective for high-throughput screening of potential influenza antivirals.

The spread of highly pathogenic avian influenza across geographical and species barriers underscores the increasing need for novel antivirals to compliment vaccination and existing antiviral therapies. Identification of new antiviral lead compounds depends on robust primary assays for high-throughput screening (HTS) of large compound libraries. We have developed a cell-based screen for potential influenza antivirals that measures the cytopathic effect (CPE) induced by influenza virus (A/Udorn/72, H3N2) infection in Madin Darby canine kidney (MDCK) cells using the luminescent-based CellTiter Glo system. This 72 h assay is validated for HTS in 384-well plates and performs more consistently and reliably than methods using neutral red, with Z values>0.8, signal-to-background>30 and signal-to-noise>10. In a blinded pilot screen (n=10,781) at 10 microM concentration, four compounds (with previously demonstrated efficacy against influenza) inhibited viral-induced CPE by >50%, with EC50/CC50 values comparable to those determined by other cell-based assays, thereby validating this assay accuracy and ability to simultaneously evaluate compound cellular availability and/or toxicity. This assay is translatable for screening against other influenza strains, such as avian flu, and may facilitate identification of antivirals for other viruses that induce CPE, such as West Nile or Dengue.

Animals↗
PubMed2005

Loss of annexin A1 expression in human breast cancer detected by multiple high-throughput analyses.

To test the efficacy of combined high-throughput analyses (HTA) in target gene identification, screening criteria were set using >fivefold difference by microarray and statistically significant changes (p<0.01) in SAGE and EST. Microarray analysis of two normal and seven breast cancer samples found 129 genes with >fivefold changes. Further SAGE and EST analyses of these genes identified four qualified genes, ERBB2, GATA3, AGR2, and ANXA1. Their expression pattern was validated by RT-PCR in both breast cell lines and tissue samples. Loss of ANXA1 in breast cancer was further confirmed at mRNA level by Human Breast Cancer Tissue Profiling Array and at protein level by immunohistochemical staining. This study demonstrated that combined HTA effectively narrowed the number of genes for further study, while retaining the sensitivity in identifying biologically important genes such as ERBB2 and ANXA1. A distinctive loss of ANXA1 in breast cancer suggests its involvement in maintaining normal breast biology.

Algorithms↗
PubMed2001

A strategy for high throughput HLA-DQ typing.

We have developed a high throughput HLA typing methodology that is a modification of the standard sequence-specific primer method. This approach is distinct from other methods using an automated DNA analyzer, as more than one gene is typed in a single lane. We have optimized the method for use on an ABI 373 automated genotyping machine. Primers were designed to preferentially amplify DNA fragments of the generic allelic groups of the DQA1 and DQB1 loci. PCR products representing alleles at the DQA1 locus were amplified using a different fluorescent dye than the PCR products from the DQB1 locus. Only three PCR reactions are required for low resolution typing of DQA1 and DQB1. Use of different labeled primers enables genotyping for both loci in a single gel lane, allowing for 64 samples to be typed at low resolution for both DQA1 and DQB1 on a single gel. Automated allele assignments were determined based on DNA migration distance through a polyacrylamide gel using a standard genotype allele-calling program. Accuracy of this method is greater than 98% for both loci. The strategy described here may be adapted to include more loci or to produce higher resolution typing of alleles encoded by these loci. It can be readily optimized for use on other slab gel or capillary electrophoresis systems.

Alleles↗
PubMed2002

High-throughput crystallization and structure determination in drug discovery.

High-throughput protein X-ray crystallography offers an unprecedented opportunity to facilitate drug discovery. The key bottlenecks in the path from target gene to three-dimensional protein structure determination are defined. Special emphasis is placed on the concept that drug discovery projects are typically directed at a key protein target whose structure must be solved within a reasonable time frame to have an impact on the drug discovery process. The time-sensitive nature of structural data has placed growing pressure on the need to automate all aspects of protein crystallography, from gene identification to model building and refinement. Current technological innovations and strategies for automation are discussed with respect to the bottleneck they are intended to eliminate.

Automation↗