Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “high throughput”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31Linked to original sources
PubMed2005

High-throughput target discovery using cell-based genetics.

High-throughput target discovery requires robust disease models and the ability to rapidly survey the genome for function. In the post-genomics era, there has been a strong emphasis placed upon "gene-to-function" approaches that take advantage of the large amount of gene sequence information now available. Here, we advocate a return to "function-to-gene" approaches as a first step in target discovery (and validation), followed by hypothesis-driven research to validate new targets identified by their activity in cell-based disease models.

Animals↗
PubMedDate not supplied

Imaging polarimetry for high throughput chiral screening.

Imaging polarimetry was demonstrated as a highly parallel method of determining optical rotation of biochemical samples. The imaging polarimeter utilized a bright, uniform light source wavelength-filtered to near the sodium D line, a sample array flanked by inlet and analyzing polarizers, and a CCD camera fitted with an equal-perspective telecentric lens. The prototype apparatus was demonstrated to have an optical resolution better than 0.08 degrees. The potential for high throughput screening was demonstrated by imaging chiral solutions in 1536-well microtiter plates and by real-time monitoring of 30 simultaneous chiral enzymatic reactions. Improvements in polarizer and CCD technology may broadly expand the technique's applicability to fields such as directed evolution and combinatorial chemistry, where screening throughput is currently limiting for chiral applications.

Algorithms↗
PubMed2005

High-throughput investigation and characterization of cobalt carboxy phosphonates.

High-throughput methods have been employed to study the system Co(2+)/(H(2)O(3)PCH(2))(2)NCH(2)C(6)H(4)COOH/NaOH in detail. The use of the phosphonocarboxylic acid (H(2)O(3)PCH(2))(2)NCH(2)C(6)H(4)COOH has led to several new cobalt carboxyaryl phosphonates under hydrothermal conditions. In addition to the effect of the pH of the starting mixture, the influence of the counterions of the cobalt salts on the product formation was investigated. Thus, reaction trends as well as fields of formation could be identified. Four new compounds Co(2)[(O(3)PCH(2))(2)NCH(2)C(6)H(4)COOH].H(2)O (1), Co[(O(3)PCH(2))(OCH)NCH(2)C(6)H(4)COOH].H(2)O (2), Co[H(2)(O(3)PCH(2))(2)NCH(2)C(6)H(4)COOH] (3), and [Co(2)(O(3)PCH(2))(2)NCH(2)C(6)H(4)COOH].3.5H(2)O (4) were obtained, and compounds 1 and 2 could be isolated as single crystals suitable for single-crystal X-ray diffraction. The counterions of the cobalt salts have an influence on the structure of the resulting compounds. This is due to the effect on the initial pH as well as the possibility of the counterions to take part in redox reactions. Compounds 1 and 4 are formed under more basic conditions, and the phosphonic acid group is fully deprotonated. The structure of 1 is a rare example of the family of inorganic-organic hybrid materials with iminobis(methylphosphonic acid) units wherein the nitrogen coordinates to the metal center. Compound 2 is the result of an in situ oxidation of one of the P-C bonds; the organic building unit is stabilized by complexation of the cobalt ion. On the basis of spectroscopic, thermogravimetric, elemental chemical analysis, and EDX-analysis data, compound 3 has been characterized as Co[H(2)(O(3)PCH(2))(2)NCH(2)C(6)H(4)COOH] and compound 4 as [Co(2)(O(3)PCH(2))(2)NCH(2)C(6)H(4)COOH].3.5H(2)O. X-ray powder diffraction and IR-spectroscopic studies show that thermal treatment of 4 leads to the title compound 1. This transformation is accompanied by a change of color from pink to deep blue.

Journal Article↗
PubMedDate not supplied

Expression profiling of herpesvirus and vaccinia virus proteins using a high-throughput baculovirus screening system.

We have developed a high-throughput system for generating baculoviruses and testing the expression, solubility, and affinity column purification of encoded proteins. We have used this system to generate baculoviruses for and analyze the expression of 337 proteins from three different herpesviruses (HSV-1, EBV, and CMV) and vaccinia virus. Subsets of these proteins were also tested for expression and solubility in E. coli. Comparisons of the results in the two systems are presented for each virus.

Animals↗
PubMed2006

A high-throughput screening assay for hydroxynitrile lyase activity.

A high-throughput screening assay for hydroxynitrile lyase activity accepting a wide range of HNL-substrates is presented, which is useful either for enzyme fingerprinting or screening of huge variant libraries generated in metagenome or directed evolution approaches.

Aldehyde-Lyases↗
PubMedDate not supplied

High throughput cryopreservation of 140,000 Physcomitrella patens mutants.

A high throughput protocol was established to preserve 140,000 mutants of a moss, Physcomitrella patens, a model plant for functional genomics studies, over liquid nitrogen. Regarding the reliable long-term storage of diverse mutant phenotypes, as well as time and cost effectiveness, each working step was optimized: 1) plant preparation, 2) freezing regime, cryogenic conditions, 3) regrowth after thawing. A prerequisite for maximum regrowth was a 1-week preculture of chopped plant material on a supplemented medium prior to freezing. Cryo vials as preculture vessels resulted in identical regrowth rates, compared to petri dishes. The cryo vial type had a significant influence on regrowth rates. A cooling rate of - 1 degrees C/min down to - 35 degrees C with a 10 min holding time before transferring plants to - 152 degrees C was the most suitable freezing regime. This protocol allows a cryopreservation of 1100 plants during a 5-day working week, practicable by one person. For more than 650 cryopreserved mutants a maximum regrowth rate of 100 % was obtained, independently of mutant phenotypes.

Bryopsida↗
PubMed2003

Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments.

A control system for high-throughput protein crystallography experiments has been developed based on a multilevel secure (SSL v2/v3) UNIX socket under the Linux operating system. Main features of protein crystallography experiments (purification, crystallization, loop preparation, data collecting, data processing) are dealt with by the software. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data, that are stored in Network File Server) in a relational database (MySQL). The system consists of several servers and clients. TCP/IP secure UNIX sockets with four predefined behaviors [(a) listening to a request followed by a reply, (b) sending a request and waiting for a reply, (c) listening to a broadcast message, and (d) sending a broadcast message] support communications between all servers and clients allowing one to control experiments, view data, edit experimental conditions and perform data processing remotely. The usage of the interface software is well suited for developing well organized control software with a hierarchical structure of different software units (Gaponov et al., 1998), which will pass and receive different types of information. All communication is divided into two parts: low and top levels. Large and complicated control tasks are split into several smaller ones, which can be processed by control clients independently. For communicating with experimental equipment (beamline optical elements, robots, and specialized experimental equipment etc.), the STARS server, developed at the Photon Factory, is used (Kosuge et al., 2002). The STARS server allows any application with an open socket to be connected with any other clients that control experimental equipment. Majority of the source code is written in C/C++. GUI modules of the system were built mainly using Glade user interface builder for GTK+ and Gnome under Red Hat Linux 7.1 operating system.

Crystallography↗
PubMed2000

Detection of oligonucleotide-ligand complexes by ESI-MS (DOLCE-MS) as a component of high throughput screening.

With the advent of combinatorial chemistry and high throughput screening, a major bottleneck in the pharmaceutical industry has changed from quickly finding active compounds to limiting them to a manageable number for proper follow-up. With hundreds to thousands of active compounds identified by a multitude of biological screens, there need to be rapid and unambiguous methods for eliminating false positive, toxic, or otherwise difficult compounds from further scrutiny. We have used electrospray ionization mass spectrometry as a rapid screening method to identify compounds from viral screens that yield a positive assay response by interaction with DNA rather than inhibiting the target enzyme. Both the sample preparation and data acquisition have been automated, allowing the screening of all hits from relevant biological screens (up to 1,000/week). The assay was validated using several known DNA intercalators and minor groove binders. These "standards" and many but not all of our "active compounds" were shown to form noncovalent complexes with a variety of different DNA:DNA and DNA:RNA duplexes.

Base Sequence↗
PubMed2006

Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery.

The aim of virtual high throughput screening is the identification of biologically relevant molecules amongst either tangible or virtual (large) collections of compounds. Amongst the various virtual screening approaches, those that are ligand based are becoming very popular due to the possibility to screen millions of molecules in a timely way. Descriptors and methods are briefly introduced and reviewed with more emphasis for those approaches that are based on fingerprint descriptors and that seems to be more utilized during the drug discovery process.

Artificial Intelligence↗
PubMed2002

A probabilistic approach to high throughput drug discovery.

A methodology is presented in which high throughput screening experimental data are used to construct a probabilistic QSAR model which is subsequently used to select building blocks for a virtual combinatorial library. The methodology is based upon statistical probability estimation and not regression. The methodology is applied to the construction of two focused virtual combinatorial libraries: one for cyclic GMP phosphodiesterase type V inhibitors and one for acyl-CoA:cholesterol O-acyltransferase inhibitors. The results suggest that the methodology is capable of selecting combinatorial substituents that lead to active compounds starting with binary (pass/fail) activity measurements.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed2004

[The role of high throughput screening in the early stage of drug research].

High throughput screening (HTS) became an integral part of the early phase drug discovery process. Although the methodology itself is widely accepted as a powerful tool of lead discovery there are a number of positive and also negative opinions associated to its application. This paper gives a short introduction to HTS technology, summarizes primary experiences and points out latest changes in screening strategy and technology. Development and application of the new screening facility of Gedeon Richter is also reported.

Animals↗
PubMed2002

Gene expression profile of human bone marrow stromal cells: high-throughput expressed sequence tag sequencing analysis.

Human bone marrow stromal cells (HBMSC) are pluripotent cells with the potential to differentiate into osteoblasts, chondrocytes, myelosupportive stroma, and marrow adipocytes. We used high-throughput DNA sequencing analysis to generate 4258 single-pass sequencing reactions (known as expressed sequence tags, or ESTs) obtained from the 5' (97) and 3' (4161) ends of human cDNA clones from a HBMSC cDNA library. Our goal was to obtain tag sequences from the maximum number of possible genes and to deposit them in the publicly accessible database for ESTs (dbEST of the National Center for Biotechnology Information). Comparisons of our EST sequencing data with nonredundant human mRNA and protein databases showed that the ESTs represent 1860 gene clusters. The EST sequencing data analysis showed 60 novel genes found only in this cDNA library after BLAST analysis against 3.0 million ESTs in NCBI's dbEST database. The BLAST search also showed the identified ESTs that have close homology to known genes, which suggests that these may be newly recognized members of known gene families. The gene expression profile of this cell type is revealed by analyzing both the frequency with which a message is encountered and the functional categorization of expressed sequences. Comparing an EST sequence with the human genomic sequence database enables assignment of an EST to a specific chromosomal region (a process called digital gene localization) and often enables immediate partial determination of intron/exon boundaries within the genomic structure. It is expected that high-throughput EST sequencing and data mining analysis will greatly promote our understanding of gene expression in these cells and of growth and development of the skeleton.

Bone Marrow Cells↗
PubMed2005

High throughput coagulation analyzers review.

The increasing no. of ordered coagulation screening tests has led to a remarkable improvement in the efficiency of automated coagulation testing, and appearance of a new generation of high throughput analyzers ensuring accuracy and precision, and reducing the strain and human error. The earliest analyzers operated mechanically, using the hook to detect the clot in the cuvette are now replaced with more sophisticated analyzer that simultaneously uses the clotting, chromogenic, and immunological principles, to provide a versatile test menu covering antigenic and functional aspects of coagulation. The armamentarium of coagulation testing is complimented with tools like; automated platelet function analyzer, flowcytometer, and molecular techniques including the polymerase chain reaction, and lately the microarrary (biochip) technology. This review addresses the principle of operation and distinctive features of various automated high throughput coagulation analyzers, their impact on improving efficiency, eliminating preanalytical and postanalytical handling thus maximizing productivity and return on investment.

Automation↗
PubMed2006

A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors.

The low rate of homologous recombination exhibited by wild-type strains of filamentous fungi has hindered development of high-throughput gene knockout procedures for this group of organisms. In this study, we describe a method for rapidly creating knockout mutants in which we make use of yeast recombinational cloning, Neurospora mutant strains deficient in nonhomologous end-joining DNA repair, custom-written software tools, and robotics. To illustrate our approach, we have created strains bearing deletions of 103 Neurospora genes encoding transcription factors. Characterization of strains during growth and both asexual and sexual development revealed phenotypes for 43% of the deletion mutants, with more than half of these strains possessing multiple defects. Overall, the methodology, which achieves high-throughput gene disruption at an efficiency >90% in this filamentous fungus, promises to be applicable to other eukaryotic organisms that have a low frequency of homologous recombination.

DNA Primers↗
PubMed2026

High-throughput single-cell proteomics and transcriptomics from same cells with a nanoliter-scale, spin-transfer approach.

Single-cell multiomic platforms provide a comprehensive snapshot of cellular states and cell types by offering critical insights into the spatiotemporal regulation of biomolecular networks at a systems level, thereby defining the basis of multicellularity. Here, we introduce nanoSPINS, an advanced platform that enables high-throughput profiling and integrative analysis of the transcriptome and proteome from the same single cells using RNA sequencing and isobaric labeling LC-MS-based proteomics, respectively. NanoSPINS can efficiently transfer mRNA-containing droplets across two microarrays via a centrifugation-based approach, while proteins are retained on the initial platform. Benchmarking of nanoSPINS on two cell lines demonstrates its ability to generate global proteomic and transcriptomic profiles that align well with previously established methodologies/platforms. The incorporation of isobaric TMTpro labeling into this single-cell multiomics platform significantly enhances the throughput of single-cell proteomic analyses. Through the high-throughput quantification of the proteome and transcriptome, nanoSPINS not only facilitates the identification of molecular features at both mRNA and protein level but also provides larger sample sizes for improved statistical power in clustering and differential abundance. Given the broad applicability of single-cell multiomics in biological research and clinical settings, we believe nanoSPINS represents a powerful platform for the characterization of heterogeneous cell populations.

Single-Cell Analysis↗
PubMed2001

Population-based screening for rare mutations: high-throughput DNA extraction and molecular amplification from Guthrie cards.

To determine the population-based frequency of a rare mutation (the 121ins2 mutation in the surfactant protein B gene), we developed high-throughput techniques to extract reliably and rapidly amplifiable DNA from Guthrie cards. Using a 3-mm punch from each of 10,044 Guthrie cards obtained from the Missouri Department of Health, we extracted DNA with deionized water by heating in the presence of 2% Chelex in a 96-well format. Average yield of DNA from each punch was 52.6 +/- 21 microg. Using 36mer primers and a 10-microL reaction volume, we amplified a 354-bp fragment of the surfactant protein B gene that contained the mutation and identified the mutation by its susceptibility to restriction enzyme digestion with SfuI. The procedure required 5 h per 96 samples but only 2 h of technician time. The amplification rate on the first attempt was 99.2%. Based on detection of eight individuals heterozygous for the mutation (confirmed by direct sequencing), we estimate the allele frequency to be 0.8/1000 individuals, an estimate not significantly different from previous estimates based on independent methods. High-throughput DNA extraction and amplification will permit establishment of DNA banks as well as efficient estimation of population-based genotype frequency for both rare and common genetic disorders.

Base Sequence↗
PubMedDate not supplied

Fourier transform infrared imaging for high-throughput analysis of pharmaceutical formulations.

Fourier transform infrared (FTIR) spectroscopic imaging with infrared array detectors has recently emerged as a powerful materials characterization tool. We report a novel application of FTIR imaging for high-throughput analysis of materials under controlled environment. This approach combines the use of spectroscopic imaging with an attenuated total reflection (ATR)-IR cell, microdroplet sample deposition system, and a device that controls humidity inside the cell. By this approach, it was possible to obtain "chemical snapshots" from a spatially defined array of many different polymer/drug formulations (more than 100) under identical conditions. This method provides direct measurement of materials properties for high-throughput formulation design and optimization. Simultaneous response (water sorption, crystallization, etc.) of the array of formulations to the environmental parameters was studied. Implications of the presented approach range from studies of smart polymeric materials and sensors to screening of pharmaceuticals and biomaterials.

Calibration↗
PubMed2006

Tissue microarray: an effective high-throughput method to study the placenta for clinical and research purposes.

OBJECTIVE: Tissue microarray (TMA) technology allows simultaneous examination of the expression of many molecular markers (protein, mRNA, DNA, etc.) with high-throughput. The application of this technology, to date, has been largely confined to the study of cancer. Placental pathology poses unique challenges because of the size of the organ, its complex anatomy, as well as its histological heterogeneity. The objective of this study was to assess the feasibility and efficiency of TMAs for immunohistochemistry and in situ hybridization of placental tissues. STUDY DESIGN: TMAs were constructed using an automated tissue arrayer. Standard 0.6-mm or 1-mm microarray needles were used. Villous parenchyma, basal plate, and chorioamniotic membranes were targeted in each block. Five mum-thick TMA sections underwent immunohistochemical analysis of both cytoplasmic and nuclear antigens using a panel of antibodies against a variety of cytoplasmic [cytokeratin-7, vascular endothelial growth factor (VEGF), and protein Z], membranous (endoglin), and nuclear (c-fos and c-jun) antigens. mRNA in situ hybridization for surfactant protein A (SP-A) and chromogenic in situ hybridization for the Y chromosome (DYZ1) were also performed. RESULTS: Validation of TMA immunoreactivity demonstrated comparable results with corresponding whole sections. When a two-tiered scoring system (positive/negative) was employed, there was agreement between two and three cores and whole tissue sections (kappa>0.7). When a three-tiered scoring system (negative, weak-positive, or strong-positive) was used, the data from three cores showed the highest agreement with whole tissue sections (kappa >0.7). In situ hybridization experiments for mRNA and DNA were also successful in that the signals were readily detectable. Successful transfer from the donor block to the recipient block differed according to the anatomical compartment. The transfer efficiency of villous parenchyma, basal plate, and chorioamniotic membranes were 96.9% (875/903), 76.7% (115/150), and 75.4% (224/297), respectively. CONCLUSION: TMA is a practical and effective tool for high-throughput molecular analysis of the human placenta. Duplicate and triplicate cores offer agreement with whole tissue sections for two-category distinction immunostaining. TMA also affords relevant results from in situ hybridization experiments for mRNA and DNA. The major advantages are the conservation of tissues and reagents, simultaneous comparison of molecular markers in different anatomical compartments of the placenta, and reduction of experimental error.

Biomarkers↗