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Results for “high throughput”

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At least 1,297 records · Page 72Linked to original sources
PubMed1999

Genomics for food biotechnology: prospects of the use of high-throughput technologies for the improvement of food microorganisms.

Functional genomics is currently the most effective approach for increasing the knowledge at the molecular level of metabolic and adaptive processes in whole cells. High-throughput technologies, such as DNA microarrays, and improved two-dimensional electrophoresis methods combined with tandem mass-spectroscopy, supported by bioinformatics, are useful tools for food biotechnology, which depends on detailed knowledge of the properties of food microbes (and pathogens) in their industrial, food and consumer environments. Genomics of food microbes, based on rapidly emerging genome sequence information, generates valuable knowledge that can be used for metabolic engineering, improving cell factories and development of novel preservation methods. Furthermore, pre- and probiotic studies, characterization of stress responses, studies of microbial ecology and, last but not least, development of novel risk assessment procedures will be facilitated.

Bacillus subtilis↗
PubMed2004

High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results.

With the increasing availability of de novo sequencing algorithms for interpreting high-mass accuracy tandem mass spectrometry (MS/MS) data, there is a growing need for programs that accurately identify proteins from de novo sequencing results. De novo sequences derived from tandem mass spectra of peptides often contain ambiguous regions where the exact amino acid order cannot be determined. One problem this poses for sequence alignment algorithms is the difficulty in distinguishing discrepancies due to de novo sequencing errors from actual genomic sequence variation and posttranslational modifications. We present a novel, mass-based approach to sequence alignment, implemented as a program called OpenSea, to resolve these problems. In this approach, de novo and database sequences are interpreted as masses of residues, and the masses, rather than the amino acid codes, are compared. To provide further flexibility, the masses can be aligned in groups, which can resolve many de novo sequencing errors. The performance of OpenSea was tested with three types of data: a mixture of known proteins, a mixture of unknown proteins that commonly contain sequence variations, and a mixture of posttranslationally modified known proteins. In all three cases, we demonstrate that OpenSea can identify more peptides and proteins than commonly used database-searching programs (SEQUEST and ProteinLynx) while accurately locating sequence variation sites and unanticipated posttranslational modifications in a high-throughput environment.

Algorithms↗
PubMed2003

High throughput detection of small genomic insertions or deletions by Pyrosequencing.

Small insertions or deletions of nucleotides are common polymorphic variations in the human genome and can result in a predisposition to disease. However, high throughput methods for detecting these variations are limited. This report describes a method to detect this variation based on sequencing the boundaries of nucleotide alterations using the Pyrosequencing technique. This method can optimally detect up to 100 base pair nucleotide insertions and deletions, and also complicated genomic rearrangements.

Algorithms↗
PubMed2004

A high-throughput approach to lanthanide complexes and their rapid screening in the ring opening polymerisation of caprolactone.

Libraries of lanthanide complexes supported by nitrogen and oxygen containing ligands have been synthesised using a high-throughput approach. The complexes were employed in the ring-opening polymerisation of epsilon-caprolactone, in some cases giving polycaprolactone of controlled molecular weight and narrow polydispersity. The libraries, based on twenty-one ligands and eight lanthanide reagents, were developed in order to determine the best combination of lanthanide metal and ligand. They were prepared via transamination reactions of [Ln[N(SiMe(3))(2)](3)] complexes with tetradentate dianionic ligands containing oxygen and nitrogen donors. 1H NMR spectroscopy was used to screen polymerisation activity. The steric demand of the ligand has a significant effect on the polymerisation process, as do the type of nitrogen donor and the size of the central Ln(3+) ion. Ligands containing aryl rings with bulky substituents such as tert-pentyl groups afforded species capable of performing controlled polymerisation of caprolactone, whereas less bulky groups such as methyl were not effective. Yttrium and mid-sized lanthanides such as samarium showed increased activity compared with the larger lanthanides, lanthanum and praseodymium, and the smaller lanthanides like ytterbium. X-ray crystal structures of a sterically demanding chelating amine-bis((2-hydroxyaryl)methyl) ligand and a chloride bridged dinuclear gadolinium complex are reported. The centrosymmetric molecule contains gadolinium in distorted capped trigonal prismatic environments bonded to two amine, two phenolate, one THF and two chloride donors.

Journal Article↗
PubMed2005

A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization.

Crystallization trials at the Division of Structural Biology in Oxford are now almost exclusively carried out using a high-throughput workflow implemented in the Oxford Protein Production Facility. Initial crystallization screening is based on nanolitre-scale sitting-drop vapour-diffusion experiments (typically 100 nl of protein plus 100 nl of reservoir solution per droplet) which use standard crystallization screening kits and 96-well crystallization plates. For 294 K crystallization trials the barcoded crystallization plates are entered into an automated storage system with a fully integrated imaging system. These plates are imaged in accordance with a pre-programmed schedule and the resulting digital data for each droplet are harvested into a laboratory information-management system (LIMS), scored by crystal recognition software and displayed for user analysis via a web-based interface. Currently, storage for trials at 277 K is not automated and for imaging the crystallization plates are fed by hand into an imaging system from which the data enter the LIMS. The workflow includes two procedures for nanolitre-scale optimization of crystallization conditions: (i) a protocol for variation of pH, reservoir dilution and protein:reservoir ratio and (ii) an additive screen. Experience based on 592 crystallization projects is reported.

Animals↗
PubMed2004

Ruleminer: a knowledge system for supporting high-throughput protein function annotations.

In this paper, we present RuleMiner, a knowledge system to facilitate a seamless integration of multi-sequence analysis tools and define profile-based rules for supporting high-throughput protein function annotations. This system consists of three essential components, Protein Function Groups (PFGs), PFG profiles and rules. The PFGs, established from an integrated analysis of current knowledge of protein functions from Swiss-Prot database and protein family-based sequence classifications, cover all possible cellular functions available in the database. The PFG profiles illustrate detailed protein features in the PFGs as in sequence conservations, the occurrences of sequence-based motifs, domains and species distributions. The rules, extracted from the PFG profiles, describe the clear relationships between these PFGs and all possible features. As a result, the RuleMiner is able to provide an enhanced capability for protein function analysis, such as results from the integrated sequence analysis tools for given proteins can be comparatively analyzed due to the clear feature-PFG relationships. Also, much needed guidance is readily available for such analysis. If the rules describe one-to-one (unique) relationships between the protein features and the PFGs, then these features can be utilized as unique functional identifiers and cellular functions of unknown proteins can be reliably determined. Otherwise, additional information has to be provided.

Algorithms↗
PubMed2006

High-throughput selection system for assessing the activity of epoxide hydrolases.

Crucial to the success of directed evolution of enantioselective enzymes for use as catalysts in synthetic organic chemistry is the availability of high-throughput assays for determining the enantiopurity of thousands of samples. Although several such ee-assays are available, they entail time and effort, which means that pre-tests for activity have been developed to eliminate non-active mutants prior to ee-screening. Pre-selection systems may be even more efficient and simple to perform. In the present paper an efficient pre-selection test for assessing the activity of epoxide hydrolases has been developed. The bacterial (E. coli) growth on agar plates is shown to be directly related to the presence of active epoxide hydrolases which catalyze the detoxicating hydrolysis of the epoxide substrates. Visual inspection of agar plates is all that is necessary to identify positive (active) hits in large libraries of mutant epoxide hydrolases.

Combinatorial Chemistry Techniques↗
PubMed1993

New instruments for high throughput receptor binding assays.

The TopCount Microplate Scintillation Counter and the Matrix 9600 Direct Beta Counter are microplate compatible instruments developed to meet the needs of investigators using radioisotope assays adapted for very high throughput. This paper describes these instruments and their application to receptor binding assays. When combined with the appropriate sample handling equipment and filter media, use of these multi-detector instruments improves sample handling efficiency and shortens overall counting time. The assay protocols including filtration through glass fiber mats and membrane filters have been investigated. Results obtained from these new instruments are compared to standard techniques using conventional liquid scintillation and gamma counting.

Filtration↗
PubMed2002

An evaluation of fluorescence polarization and lifetime discriminated polarization for high throughput screening of serine/threonine kinases.

We used two kinases, c-jun N terminal kinase (JNK-1) and protein kinase C (PKC), as model enzymes to evaluate the potential of fluorescence polarization (FP) for high-throughput screening and the susceptibility of these assays to compound interference. For JNK-1 the enzyme kinetics in the FP assay were consistent with those found in a [gamma-33P]ATP filter wash assay. Determined pIC(50)s for nonfluorescent JNK-1 inhibitors were also consistent with those found in the filter wash assay. In contrast, fluorescent compounds were found to interfere with the JNK-1 FP assay, appearing as false positives, defined by their lack of activity in the filter wash assay. We also developed a second assay using a different kinase, protein kinase C, which was used to test a 5000 compound diversity set. As for JNK-1, interference from fluorescent compounds caused a high false positive rate. The Molecular Devices Corporation 'FLARe' instrument is capable of discriminating between fluorophores on the basis of their fluorescence (excited state) lifetime, and may assist in reducing compound interference in fluorescent assays. In both model FP kinase assays described here some, although not complete, reduction in interference from fluorescent compounds was achieved by the use of FLARe.

Activating Transcription Factor 2↗
PubMed2003

Determining appropriate substrate conversion for enzymatic assays in high-throughput screening.

It is generally accepted that the conversion of substrate should be kept at less than 10% of the total substrate used when studying enzyme kinetics. However, 10% or less substrate conversion often will not produce sufficient signal changes required for robust high-throughput screening (HTS). To increase the signal-to-background ratio, HTS is often performed at higher than 10% substrate conversion. Because the consequences of high substrate conversion are poorly understood, the screening results are sometimes questioned by enzymologists. The quality of an assay is judged by the ability to detect an inhibitor under HTS conditions, which depends on the robustness of the primary detection signal (Z factor) and the sensitivity to an inhibitor. The assay sensitivity to an inhibitor is reflected in the observed IC(50) value or percent inhibition at a fixed compound concentration when single-point data are collected. The major concern for an enzymatic assay under high substrate conversion is that the sensitivity of the screen may be compromised. Here we derive the relationship between the IC(50) value for a given inhibitor and the percentage of substrate conversion using a first-order kinetic model under conditions that obey Henri-Michaelis-Menten kinetics. The derived theory was further verified experimentally with a cAMP-dependent protein kinase. This model provides guidance for assay developers to choose an appropriate substrate conversion in designing an enzymatic assay, balancing the needs for robust signal and sensitivity to inhibitors.

Catalysis↗
PubMed2004

High throughput screening of library compounds against an oligonucleotide substructure of an RNA target.

Approximately 300,000 compounds from selected libraries were screened against a subdomain of a hepatitis C viral (HCV) RNA using a high throughput flow injection mass spectrometry (FIA-MS) method with automated data storage and analysis. Samples contained 2 microM RNA target and 10 microM of each of up to ten ligands. Preliminary studies to optimize operational parameters used the binding of aminoglycosides to the A44 subdomain of bacterial RNA. Binding (confirmed by titration) and sensitivity were maximized within the constraints of the library and throughput. The mobile phase of 5 mM ammonium acetate in 50% isopropanol maintained the noncovalent complexes and provided good detection by electrospray mass spectrometry. Additionally, this composition maximized general solubility of the various classes of compounds including the oligonucleotide and organic library molecules. Cation adduction was insignificant in this screen although some solute and target dependent acetate adduction was observed. The ion trap mass spectrometer provided sufficient mass resolution to identify complexes of RNA with known components of the library. Converted mass spectral data (netCDF) were subjected to two types of statistical evaluation based on binding. The first algorithm identified noncovalent complexes that correlated with the molecular weights of the injected compounds. The second yielded the largest peak in the noncovalent complex region of the spectrum; this spectrum may or may not correlate with expected well components. Sixty-three compounds were confirmed to bind by more stringent secondary testing. Titrations, which were carried out with selected binding compounds, yielded a range of dissociation constants. Biological activity was observed for eleven confirmed binders.

Ligands↗
PubMedDate not supplied

Combinatorial approach toward high-throughput analysis of direct methanol fuel cells.

A 40-member array of direct methanol fuel cells (with stationary fuel and convective air supplies) was generated by electrically connecting the fuel cells in series. High-throughput analysis of these fuel cells was realized by fast screening of voltages between the two terminals of a fuel cell at constant current discharge. A large number of voltage-current curves (200) were obtained by screening the voltages through multiple small-current steps. Gaussian distribution was used to statistically analyze the large number of experimental data. The standard deviation (sigma) of voltages of these fuel cells increased linearly with discharge current. The voltage-current curves at various fuel concentrations were simulated with an empirical equation of voltage versus current and a linear equation of sigma versus current. The simulated voltage-current curves fitted the experimental data well. With increasing methanol concentration from 0.5 to 4.0 M, the Tafel slope of the voltage-current curves (at sigma=0.0), changed from 28 to 91 mV.dec-1, the cell resistance from 2.91 to 0.18 Omega, and the power output from 3 to 18 mW.cm-2.

Combinatorial Chemistry Techniques↗
PubMed2006

High throughput quantification of protein expression of cancer antigens in tissue microarray using quantum dot nanocrystals.

We developed and validated a novel method for quantifying protein expression of cancer tumors in an accurate, sensitive, and high throughput format. This technique integrates quantum dots, tissue microarray, optical spectroscopy, and algorithm design for analysis of tumor biopsies. The integration of this method for tissue analysis in the clinic bears potential impact for improving the diagnosis and treatment of cancer.

Animals↗
PubMedDate not supplied

High-throughput, fluorescence-based screening for soluble protein expression.

Protein expression screening methods are essential for proteomic scale characterization of gene and cDNA expression libraries. Screening methods are also important for the identification of highly expressed protein targets, for example, in quantities suitable for high-throughput screening and protein structural studies. To address these needs, we describe the implementation of several rapid, fluorescence-based protein expression screening strategies using Escherichia coli or E. coli-based in vitro transcription/translation (IVT) systems. In vitro expression screening is fast, convenient and, as we show, correlates well with in vivo expression. For screening, expressed proteins are labeled either as fusions with green fluorescent protein (GFP) or through translational incorporation of a fluorescent amino acid derivative, BODIPY-FL-Lysine. Fluorescence-based detection of GFP fusions or BODIPY-labeled proteins is considerably faster than other common expression screening methods, such as immunological detection of gels or dot blots. Furthermore, in vitro and in vivo screening used together yield a larger set of expressed proteins than either method alone. Specifically labeled proteins in cellular lysates are detected in one of three formats: a microplate using a fluorescence plate reader, a dot-blot using a fluorescence scanner or a microarray using a laser scanner. We have established a correlation among the various detection formats, which validates the use of protein microarrays for expression screening. Production of expressed proteins detected through screening can be scaled up either using IVT reactions or with in vivo expression systems in the absence of a fluorophore for subsequent characterization of protein function or interactions.

Boron Compounds↗
PubMed2007

An inexpensive, simple protocol for DNA isolation from blood for high-throughput genotyping by polymerase chain reaction or restriction endonuclease digestion.

We describe simple, inexpensive, and reliable methods for isolating DNA from avian blood, semen, or feather pulp. The procedures are readily applicable to high-throughput 96-well plate isolation for genotype analysis of chicken DNA based on restriction endonuclease digestion or PCR. Isolation cost is primarily the cost of a deep-well assay block and a few pipet tips; current price is less than 0.10 dollar per sample, providing a significant cost advantage over commercial kits. The procedure employs inexpensive, nonhazardous reagents and yields intact, double-stranded DNA from as little as 2 to 10 microL of avian blood, suitable for RFLP analysis or hundreds of PCR amplifications. We compared our method to published procedures for alkaline extraction from feather pulp and found our method to be more reliable with the advantage of isolating intact DNA sequences that can be easily quantified. With minor modifications, the method can isolate DNA for PCR genotyping from mammalian whole blood.

Animals↗
PubMed2006

Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies.

Surface plasmon resonance (SPR) biosensors have enabled a wide range of applications in which researchers can monitor biomolecular interactions in real time. Owing to the fact that SPR can provide affinity and kinetic data, unique features in applications ranging from protein-peptide interaction analysis to cellular ligation experiments have been demonstrated. Although SPR has historically been limited by its throughput, new methods are emerging that allow for the simultaneous analysis of many thousands of interactions. When coupled with new protein array technologies, high-throughput SPR methods give users new and improved methods to analyze pathways, screen drug candidates and monitor protein-protein interactions.

Animals↗
PubMed2004

High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis of base-specific cleavage products is an efficient, highly accurate tool for the detection of single base sequence variations. We describe the first application of this comparative sequencing strategy for automated high-throughput mutation detection in microbial genomes. The method was applied to identify DNA sequence changes that occurred in Escherichia coli K-12 MG1655 during laboratory adaptive evolution to new optimal growth phenotypes. Experiments were based on a genome-scale in silico model of E. coli metabolism and growth. This model computes several phenotypic functions and predicts optimal growth rates. To identify mutations underlying a 40-d adaptive laboratory evolution on glycerol, we resequenced 4.4% of the E. coli-K12 MG1655 genome in several clones picked at the end of the evolutionary process. The 1.54-Mb screen was completed in 13.5 h. This resequencing study is the largest reported by MALDI-TOF mass spectrometry to date. Ten mutations in 40 clones and three deviations from the reference sequence were detected. Mutations were predominantly found within the glycerol kinase gene. Functional characterization of the most prominent mutation shows its metabolic impact on the process of adaptive evolution. All sequence changes were independently confirmed by genotyping and Sanger-sequencing. We demonstrate that comparative sequencing by base-specific cleavage and MALDI-TOF mass spectrometry is an automated, fast, and highly accurate alternative to capillary sequencing.

Adaptation, Biological↗
PubMed2001

Asymmetric activation of chiral alkoxyzinc catalysts by chiral nitrogen activators for dialkylzinc addition to aldehydes: super high-throughput screening of combinatorial libraries of chiral ligands and activators by HPLC-CD/UV and HPLC-OR/RIU systems.

Asymmetric catalysts, prepared by chiral ligand exchange or chiral modification, can evolve further into highly activated catalysts through engineering with chiral activators. Two new methodologies for "super high-throughput screening" (SHTS) of chiral ligands and activators have been developed as a combination of HPLC-CD/UV (CD/ UV = circular dichroism/ultraviolet spectroscopy) or -OR/RIU (OR/RIU = optical rotation/refractive index unit) with a combinatorial chemistry (CC) factory. With these techniques, the % ee of the product is determined within minutes without separation of the enantiomeric products by using a nonchiral stationary phase. Therefore, those SHTS techniques combined with our 'asymmetric activation' concept can provide a powerful strategy for finding the best activated chiral catalyst.

Journal Article↗