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PubMedDate not supplied

Imaging reflection IR spectroscopy as a tool to achieve higher integration for high-throughput experimentation in catalysis research.

FTIR spectroscopy in reflection mode combined with a focal plane array (FPA) detector was employed for high-throughput screening of activity of catalysts in n-pentane hydroisomerization. The reactor system was evaluated using reference catalysts Pt-MOR and gamma-alumina of known catalytic activity. By using the reflection setup, a higher degree of parallelization was possible, as compared to previous reports, in which transmission cells had been used. The 49-channel parallel reactor in combination with the FPA-IR optical setup was able to provide reliable information about the activity of different catalysts with relative data error of less than +/-20%.

Journal Article↗
PubMed2006

High-throughput synthesis and catalytic properties of a molecular sieve with 18- and 10-member rings.

Crystalline molecular sieves with large pores and high adsorption capacities have many potential applications. Of these materials, zeolites are of particular interest owing to their stability in a wide range of experimental conditions. An aluminophosphate with very large circular channels(5) containing 18 oxygen atoms (18-ring channels) has been synthesized, but in the search for large-pore zeolites, most of the materials which have been synthesized up to now contain only 14-ring channels; the synthesis of zeolites with larger ring structures has been believed to be hindered by the low Si-O-Si bond angles available. A silicogaloaluminate (ECR-34) with unidirectional 18-ring channels was recently reported, but exhibited low micropore volume, thus rendering the material less attractive for catalytic applications. Here we report the structure and catalytic activity of the silicogermanate zeolite ITQ-33; this material exhibits straight large pore channels with circular openings of 18-rings along the c axis interconnected by a bidirectional system of 10-ring channels, yielding a structure with very large micropore volume. The conditions for synthesis are easily accessible, but are not typical, and were identified using high-throughput techniques.

Journal Article↗
PubMed2006

HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.

HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The resource is primarily intended to serve computational biologists interested in building models of transcription factor binding sites from large sets of binding sequences. The guiding principle is to make available all information that is relevant for this purpose. For each experiment, we try to provide accurate information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, assembled clone sequences (concatemers) and complete sets of in vitro selected protein-binding tags. In addition, we offer in-house derived binding sites models. HTPSELEX also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols. The FTP site contains the trace archives and database flatfiles. The web server offers user-friendly interfaces for viewing individual entries and quality-controlled download of SELEX sequence libraries according to a user-defined sequencing quality threshold. HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex.

Binding Sites↗
PubMed2000

Development of high throughput screening assays using fluorescence polarization: nuclear receptor-ligand-binding and kinase/phosphatase assays.

Fluorescence polarization (FP) has been used to develop high throughput screening (HTS) assays for nuclear receptor-ligand displacement and kinase inhibition. FP is a solution-based, homogeneous technique requiring no immobilization or separation of reaction components. The FP-based estrogen receptor (ER) assay is based on the competition of fluorescein-labeled estradiol and estrogen-like compounds for binding to ER. These studies determined the Kd for this interaction to be 3 nM for ERalpha and 2 nM for ERbeta; IC50 values for 17beta-estradiol, tamoxifen, 4-OH-tamoxifen, and diethylstibestrol were determined to be 5.6, 189, 26, and 3.5 nM, respectively. In a screen of 50 lead compounds from a transcriptional activation screen, 21 compounds had IC50 values below 10 microM, with one having an almost 100-fold higher affinity for ERbeta over ERalpha. These data show that an FP-based competitive binding assay can be used to screen diverse compounds with a broad range of binding affinities for ERs. The FP-based protein-tyrosine kinase (PTK) assay uses fluorescein-labeled phosphopeptides bound to anti-phosphotyrosine antibodies. Phosphopeptides generated by a kinase compete for this binding. In c-Src kinase reactions, polarization decreased with time as reaction products displaced the fluorescein-labeled phosphopeptide from the anti-phosphotyrosine antibodies. The experimentally determined IC50 of AG 1478 was 400 pM, while Genistein did not inhibit the epidermal growth factor receptor at similar concentrations. Like the FP-based PTK assay, the protein kinase C (PKC) assay utilizes competition. PKC isoforms had different turnover rates for the peptide substrate. The IC50 for staurosporine was less than 10 nM for all PKC isoforms. Tyrosine phosphatase assays use direct binding rather than competition. Increasing concentrations of T-cell protein-tyrosine phosphatase (TC PTP) increased the rate of dephosphorylation. This change in polarization was dependent on TC PTP and was inhibited by 50 microM Na3VO4. The IC50 of Na3VO4 was 4 nM for TC PTP. These data demonstrate that a FP-based assay can detect kinase and phosphatase activity. Homogeneous, fluorescent techniques such as FP are now methods of choice for screening many types of drug targets. New HTS instrumentation and assay methods like these make FP a technology easily incorporated into HTS.

Animals↗
PubMed2000

A novel high throughput chemiluminescent assay for the measurement of cellular cyclic adenosine monophosphate levels.

The second messenger 3', 5'-cyclic AMP (cAMP) is a highly regulated molecule that is governed by G protein-coupled receptor activation and other cellular processes. Measurement of cAMP levels in cells is widely used as an indicator of receptor function in drug discovery applications. We have developed a nonradioactive ELISA for the accurate quantitation of cAMP levels produced in cell-based assays. This novel competitive assay utilizes chemiluminescent detection that affords both a sensitivity and a dynamic assay range that have not been previously reported with any other assay methodologies. The assay has been automated in 96- and 384-well formats, providing assay data that are equivalent to, if not better than, data generated by hand. This report demonstrates the application of this novel assay technology to the functional analysis of a specific G protein-coupled receptor, neuropeptide receptor Y1, on SK-N-MC cells. Our data indicate the feasibility of utilizing this assay methodology for monitoring cAMP levels in a wide range of functional cell-based assays for high throughput screening.

Cell Line↗
PubMed2004

Colorimetric high-throughput assay for alkene epoxidation catalyzed by cytochrome P450 BM-3 variant 139-3.

Cytochrome P450 BM-3 variant 139-3 is highly active in the hydroxylation of alkanes and fatty acids (AGlieder, ET Farinas, and FH Arnold, Nature Biotech 2002;20:1135-1139); it also epoxidizes various alkenes, including styrene. Here the authors describe a colorimetric, high-throughput assay suitable for optimizing this latter activity by directed evolution. The product of styrene oxidation by 139-3, styrene oxide, reacts with the nucleophile gamma-(4-nitrobenzyl)pyridine (NBP) to form a purple-colored precursor dye, which can be monitored spectrophotometrically in cell lysates. The sensitivity limit of this assay is 50-100 microM of product, and the detection limit for P450 BM-3 139-3 is ~0.2 microM of enzyme. To validate the assay, activities in a small library of random mutants were compared to those determined using an NADPH depletion assay for initial turnover rates.

Alkenes↗
PubMed2004

Miniaturization and validation of a high-throughput serine kinase assay using the AlphaScreen platform.

Reducing costs while maintaining the highest readout quality is a precept of modern high-throughput screening. Given the trend toward nonradiometric screening platforms, this has been a big challenge for some kinase target classes. Common issues include low sensitivity, susceptibility to nonspecific interference, or the need for costly reagents. In this study, the authors describe the feasibility of miniaturization of a serine kinase assay using generic reagents in the AlphaScreen format. They have validated the robustness of this assay in the course of miniaturization from a 35-to 4.375-microL final assay volume in 384-and 1536-well formats. Within this volume range, they consistently obtained Z' values above 0.5 and have investigated the suitability of these assay formats for measuring compound effects by testing a set of 25 previously identified active compounds. These active compounds were also reliably identified in the miniaturized assay formats. The results presented here show that the AlphaScreen technology permits robust and cost-efficient miniaturization of serine/threonine kinase assays.

Animals↗
PubMed2005

Interpretation of high-throughput liquid chromatography mass spectrometry data for quality control analysis and analytical method development.

An approach to rapidly process and interpret high-throughput liquid chromatography mass spectrometry data is presented. This approach applies an in-house developed computer application to process LC-MS report files containing spectral and chromatographic data from four different detectors (i.e. electrospray positive ionization, electrospray negative ionization mass spectrometry, UV absorption, and evaporative light scattering detection). Properties characteristic of detection and chromatographic retention are extracted and populated into a database. Approaches to applying this analytical information database for quality control analysis of ca. 400,000 samples are presented. Compound quality assessment methods employing average purity and detection data fields are compared to methods employing multiple quality control criteria (e.g. detection, purity, retention, and signal to noise). Structural similarity searches were applied with the analytical information database to identify compounds that may be undetectable by electrospray mass spectrometry. In addition, an approach to applying the database to aid in the selection of analytical detection and chromatography conditions for rapid analytical method development is also discussed.

Chromatography, Liquid↗
PubMedDate not supplied

High-throughput determination of seven trace elements in food samples by inductively coupled plasma-mass spectrometry.

A method was developed for high-throughput determinations of 7 elements in food samples, namely antimony (Sb), arsenic (As), cadmium (Cd), chromium (Cr), lead (Pb), mercury (Hg), and tin (Sn). The samples were digested by closed-vessel microwave-assisted digestion using concentrated nitric acid (HNO3) as the medium, followed by microwave- assisted evaporation to concentrate the sample solutions before dilution to the desired volume. The microwave-assisted evaporation procedure effectively reduced the final acid concentration to around 8% before analysis by inductively coupled plasma-mass spectrometry (ICP-MS). This reduction allows determination by ICP-MS to proceed without further sample dilution, which would affect the detection limit. The method was validated, and method recoveries for As, Cd, Cr, Pb, and Hg were within the certified ranges of the chosen certified reference materials. Recoveries of the 7 elements from spiked samples ranged from 93.1 to 103.6%. The standard uncertainties of precision for the 7 elements were between 3.1 and 4.3%. Interlaboratory comparison studies for As, Cd, and Pb gave z-scores ranging from -0.2 to 0.3.

Calibration↗
PubMed2025

SMART-RNA-Metavirome: a practical RNA metavirome platform compatible with high-throughput sequencing of both short and long reads.

BACKGROUND: The RNA virosphere's extensive diversity and its role in emerging infectious diseases underscore the importance of non-targeted sequencing for identifying unknown or rare pathogens, including co-infections. However, enriching low-abundance viral sequences in RNA metaviromics, particularly in the preparation of cDNA libraries and their compatibility with next-generation sequencing (NGS) and third-generation sequencing (TGS), remains challenging. Therefore, our objective is to develop and systematically assess a practical RNA metavirome methodology specifically tailored for the enrichment of low-abundance viral sequences within samples. METHODS: We developed the SMART-RNA-Metavirome platform, integrating SMART-9n library preparation with NGS and TGS technologies. Total RNA was extracted from two field-collected wild Aedes albopictus pools, along with one laboratory-infected Ae. albopictus pool harboring dengue virus (DENV). This RNA was subjected to reverse transcription using both this optimized protocol and random primer-based methods, followed by high-throughput sequencing on Illumina, Oxford Nanopore, and QitanTech Nanopore technologies. Welch's t-test was employed for comparative analysis of the subsequent RNA metavirome data, specifically to evaluate differences in viral species composition and abundance of viral reads between experimental groups. Furthermore, the effectiveness of this platform was systematically validated via RT-qPCR and SMART-RNA-Metavirome-based Oxford Nanopore sequencing across multiple sample types, including mosquito specimens from DENV-infected Ae. albopictus, serum samples from dengue patients and viral isolates of Japanese encephalitis virus (JEV) and Zika virus (ZIKV). RESULTS: The SMART-RNA-Metavirome platform has been systematically validated to excel in enriching the composition and diversity of the RNA virome (P = 0.04), providing sufficient coverage for the complete reconstruction of viral genomes. When employed in the detection of DENV-infected Ae. albopictus, clinical serum samples, and viral isolates of JEV and ZIKV, this technique exhibits a robust correlation with RT-qPCR (r2 > 0.95). Notably, it demonstrates exceptional sensitivity, ensuring sufficient coverage even in samples of DENV-infected Ae. albopictus with a Ct-value of 35.3, attaining an impressive 99.88% genome coverage. Furthermore, this platform possesses the capability to identify virus species and determine their serotypes. CONCLUSIONS: In our study, the SMART-RNA-Metavirome platform outperforms traditional methods, enriching RNA virome composition and diversity, enabling practical compatibility with both NGS and TGS technologies. It demonstrates significant proficiency in detecting both known and unknown arboviruses, even in low-titer samples such as those from wild mosquitoes and clinical sera. This platform facilitates comprehensive monitoring, risk assessment, and early warning of RNA virus transmissions, enhancing our understanding of RNA virome diversity and ecological patterns.

High-Throughput Nucleotide Sequencing↗
PubMed2001

Delay of intracellular calcium transients using a calcium chelator: application to high-throughput screening of the capsaicin receptor ion channel and G-protein-coupled receptors.

Whole-cell functional assays are often used for high-throughput screening (HTS) of molecular targets such as ion channels and G-protein-coupled receptors. A common method for assaying the activity of these membrane proteins is to measure the change in intracellular calcium concentration upon receptor stimulation. These changes in calcium concentration are typically transient and therefore not readily adapted to high-density plate formats used in HTS instruments. We have demonstrated that an intracellular calcium chelator, BAPTA, was able to delay by 5- to 20-fold and extend for several minutes the observed calcium signals initiated by extracellular calcium influx or release of calcium from intracellular stores. As examples, we used cells expressing a calcium-permeable ion channel, vanilloid receptor type 1 (the capsaicin receptor), and two G-protein-coupled receptors. These receptor-mediated increases in intracellular calcium concentration were measured by both fluorescence-based and luminescence-based detection methods. The use of an intracellular calcium chelator to delay calcium signaling should have wide application since it allows the measurement of the functional activity of any cellular receptor that signals through calcium. With this procedure, calcium fluorescence and luminescence whole-cell functional assays may be performed with standard laboratory pipetting and detection systems.

Calcium↗
PubMed2006

High-throughput screening for monoamine oxidase-A and monoamine oxidase-B inhibitors using one-step fluorescence assay.

AIM: To develop high-throughput screening (HTS) assays for monoamine oxidase (MAO)-A and MAO-B inhibitors. METHODS: A fluorescence probe based method measuring MAO-A and MAO-B activity was established and optimized, with its sensitivity, stability and specificity evaluated. Reaction conditions including enzyme sources, substrate concentrations, incubation volume and reaction time in 384-well format were optimized to achieve sensitive and low consumptive goal. RESULTS: In optimized conditions, dynamic parameters of MAO-A and MAO-B were obtained. The K(m) value of serotonin to MAO-A was 1.66 micromol/L, while that of benzylamine to MAO-B was 0.80 micromol/L. The IC(50) value of clorgyline to MAO-A was 2.99 nmol/L, and that of deprenyl to MAO-B was 7.04 nmol/L, matching those obtained from traditional spectrometric assays. Among tested samples, one compound exerted an inhibitory effect on MAO-A activity with IC(50) as 0.36 micromol/L, and three compounds had an inhibitory effect on MAO-B activity with IC(50) as 0.13, 0.19, and 0.13 micromol/L. The Z' factor was 0.71+/-0.03 and 0.75+/-0.03 in MAO-A-inhibitor and MAO-B-inhibitor HTS system, respectively. CONCLUSION: The established assays can be well applied to MAO-A and MAO-B inhibitor screening with high quality, precision and reproducibility.

Animals↗
PubMed2001

On-line sample preparation for high throughput reversed-phase LC/MS analysis of combinatorial chemistry libraries.

An on-line sample preparation method utilizing a time-programmed autosampler is described for high throughput liquid chromatography/mass spectrometry (LC/MS). This approach is particularly helpful for the LC/MS analysis of samples which require solvents incompatible with HPLC in the sample preparation process. The on-line sample preparation approach minimizes a bottleneck in throughput and improves sample recovery under some circumstances.

Chromatography, High Pressure Liquid↗
PubMed1997

Recombinant Mycobacterium aurum expressing Escherichia coli beta-galactosidase in high throughput screening of antituberculosis drugs.

Mycobacterium aurum is considered a surrogate of M. tuberculosis and recently has been proposed as test organism in high throughput screening of antituberculosis drugs (3). In this investigation, we suggest use of a recombinant M. aurum expressing E. coli lacZ gene, in which beta-galactosidase production is the reporter system as recently reported by us (6). The assay is based on production of beta-galactosidase in presence of drugs during growth. Enzyme production was inhibited within 4 h by frontline antimycobacterial drugs like streptomycin, rifampicin, isoniazid, ethambutol, ofloxacin, and sparfloxacin at their MICs. The assay could be performed conveniently in 96-well microtiter plate format.

Antitubercular Agents↗
PubMed2006

An optimal pooling strategy applied to high-throughput screening for rare marker-free transformants.

An optimal pooling system, called Accurate and Fast Target Screening, has been developed for high-throughput identifying the rare marker-free transformants. This system can identify targets between 10- and 100-fold more efficiently than analysis of individual samples. By calculating the efficiency for different proportions of targets and the optimal group size in a worst case scenario, we are able to estimate an upper limit for the number of tests that are required. The application of this system to determine the transgene in an artificially constructed population of transgenic and non-transgenic wheat lines successfully identified the 10 positive samples located randomly with 990 negative samples using only 92 PCR reactions. The same approach was also applied to determine transgene expression by SDS-PAGE of seed proteins. This system gives unambiguous positive or negative results and should facilitate marker-free transformation.

Algorithms↗
PubMed2004

A new high-throughput AFLP approach for identification of new genetic polymorphism in the genome of the clonal microorganism Mycobacterium tuberculosis.

We have here applied high-throughput amplified fragment length polymorphism (htAFLP) analysis to strains belonging to the five classical species of the Mycobacterium tuberculosis complex. Using 20 strains, three enzyme combinations and eight selective amplification primer pairs, 24 AFLP reactions were performed per strain. Overall, this resulted in 480 DNA fingerprints and more than 1200 htAFLP-amplified PCR fragments were visualised per strain. The cumulative dendrogram correctly clustered strains from the various species, albeit within a distance of 6.5% for most of them. The single isolate of Mycobacterium canettii presented separately at 19% distance. All over, 169 fragments (14%) appeared to be polymorphic. Sixty-eight were specific for M. canetti and forty-five for Mycobacterium bovis. For the 10 different M. tuberculosis strains included in the present analysis, 56 polymorphic markers were identified. Upon sequencing 20 of these marker regions and comparisons with the H37Rv genome sequence, 25% appeared to share homology to members of the antigenically variable PE/PPE surface protein encoding gene family confirming previous findings on the genetic heterogeneity within these genes. In addition, homologues for phage genes and insertion element-encoded genes were detected. Forty-five percent of the sequences derived from ORFs with a currently unknown function, which was corroborated by genome sequence comparison for the clinical M. tuberculosis CD 1551 isolate. Sequence variation in M. tuberculosis was assessed in more detail for a subset of these loci by newly designed PCR restriction fragment length polymorphism (RFLP) tests and direct sequencing. Fourteen novel PCR RFLP tests were developed and twelve novel single nucleotide polymorphisms (SNPs) were identified, all suited for epidemiological analysis of M. tuberculosis. The tests allowed for identification of the major Mycobacterium species and M. tuberculosis variants and clones.

Cluster Analysis↗
PubMed1999

Homogeneous fluorescence readouts for miniaturized high-throughput screening: theory and practice.

It is widely recognized that fluorescence techniques represent the most important future detection method for miniaturized ultra-high-throughput screening. However, such techniques encompass many different approaches, each with its own particular set of advantages and limitations. Here, the authors summarize each of the major fluorescence techniques and explain the underlying principles that form the basis for a theory-led strategy to readout selection and assay design.

Journal Article↗