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At least 361 records · Page 20Linked to original sources
PubMed2006

Automated vs manual triage for bioterrorist disaster: a blinded crossover feasibility study comparing personal digital assistant to paper-based triage.

INTRODUCTION: This article reports results of a National Institutes of Health/National Library of Medicine Small Business Innovation Research-funded research grant comparing paper-based and automated Palm handheld computer disaster triage documentation. OBJECTIVES: The aim of this study was to test the feasibility of automated handheld computer triage and compare it to handwritten triage. METHODS: A paired t test was used in an intraindividual, blinded, crossover study to compare the 2 methods of disaster triage by 2 objective measures--time and accuracy. A total of 57 experienced, licensed first responders participated. Results are from analysis of 8 disaster scenarios with a total of 400 patients triaged using the 2 methods of documentation, crossed over, blinded, and paired per participant. RESULTS: The study demonstrated the feasibility of using TriageDoc, a Palm personal digital assistant (PDA ) program, as a viable alternative to current manual disaster triage. Furthermore, the PDA program gave advantage to bioterrorist agent identification. CONCLUSIONS: The feasibility of an automated Palm (Palm, Inc., Sunnyvale, CA) PDA triage program was demonstrated in this study. Study limitations, by the number of participants and the fact it is feasibility research, are acknowledged. Nevertheless, the research demonstrated TriageDoc was as accurate or more accurate as the manual method of triage with a tendency to require less time. Also there was no statistically significant difference between research sites with respect to accuracy or time to completion when the TriageDoc system was used. The program provided consistency and had flexibility in adapting to the various differences in triage methods at different locations. Hence, PDA programs such as TriageDoc may have potential advantages over handwritten documentation for disaster triage.

Bioterrorism↗
PubMed2005

In situ DMSO hydration measurements of HTS compound libraries.

Compounds used in high throughput screening (HTS) are typically dissolved in DMSO. These solutions are stored automation-friendly racks of wells or tubes. DMSO is hygroscopic and quickly absorbs water from the atmosphere. When present in DMSO compound solutions, water can accelerate degradation and precipitation. Understanding DMSO hydration in an HTS compound library can improve storage and screening methods by managing the impact of water on compound stability. A non-destructive, acoustic method compatible with HTS has been developed to measure water content in DMSO solutions. Performance of this acoustic method was compared with an optical technique and found to be in good agreement. The accuracy and precision of acoustic measurements was shown to be under 3% over the tested range of DMSO solutions (0% to 35% water by volume) and insensitive to the presence of HTS compounds at typical storage concentrations. Time course studies of hydration for wells in 384-well and 1536-well microplates were performed. Well geometry, fluid volume, well position and atmospheric conditions were all factors in hydration rate. High rates of hydration were seen in lower-volume fills, higher-density multi-well plates and when there was a large differential between the humidity of the lab and the water content of the DMSO. For example, a 1536-well microplate filled with 2microL of 100% DMSO exposed for one hour to a laboratory environment with approximately 40% relative humidity will absorb over 6% water by volume. Understanding DMSO hydration rates as well as the ability to reverse library hydration are important steps towards managing stability and availability of compound libraries.

Acoustics↗
PubMed1996

Isotope or mass encoding of combinatorial libraries.

BACKGROUND: Combinatorial chemistry using solid-phase synthesis is a rapidly developing technology that can result in a significant reduction in the time required to find and optimize lead compounds. The application of this approach to traditional medicinal chemistry has led to the construction of libraries of small organic molecules on resin beads. A major difficulty in developing large combinatorial libraries is the lack of a facile encoding and decoding methodology to identify active compounds. RESULTS: Several encoding schemes are described which use the ability of mass spectrometry to ascertain isotopic distributions. Molecular tags are attached to resin beads in parallel or on the linker used for chemical library synthesis. The tags are encoded via a controlled ratio of a number of stable isotopes on the tagging molecules, and range from a single to a complex isotopic distribution. CONCLUSIONS: A novel coding scheme is described that is useful for the generation of large encoded combinatorial libraries. The code can be cleaved after assay and analyzed by mass spectrometry in an automated fashion. An important element of the combinatorial discovery process is the ability to extract the structure-activity relationship (SAR) information made available by library screening. The speed and sensitivity of the mass-encoding scheme has the potential to determine the full SAR for a given library.

Chemistry, Organic↗
PubMed1992

Cosmid linking clones localized to the long arm of human chromosome 11.

Molecular probes that contain DNA flanking CpG-rich restriction sites are extremely valuable in the construction of physical maps of chromosomes and in the identification of genes associated with hypomethylated HTF (HpaII tiny fragment) islands. We describe a new approach to the isolation and characterization of linking clones in arrayed chromosome-specific cosmid libraries through the large-scale semiautomated restriction mapping of cosmid clones. We utilized a cosmid library representing human chromosome 11q12-11qter and carried out automated restriction enzyme analysis, followed by regional localization to chromosome 11q using high-resolution in situ suppression hybridization. Using this approach, 165 cosmid linking clones containing one or more NotI, BssHII, SfiI, or SacII sites were identified among 960 chromosome-specific cosmids. Furthermore, this analysis allowed clones containing a single site to be distinguished from those containing clusters of two or more rare sites. This analysis demonstrated that more than 75% of cosmids containing a rare restriction site also contained a second rare restriction site, suggesting a high degree of CpG-rich restriction site clustering. Thirty chromosome 11q-specific cosmids containing rare CpG-rich restriction sites were regionally localized by high-resolution fluorescence in situ suppression hybridization, demonstrating that all of the CpG-rich sites detected by this method were located in bands 11q13 and 11q23. In addition, the distribution of (CA)n repetitive sequences was determined by hybridization of the arrayed cosmid library with oligonucleotide probes, confirming a random distribution of microsatellites among CpG-rich cosmid clones. This set of reagent cosmid clones will be useful for physical linking of large restriction fragments detected by pulsed-field gel electrophoresis and will provide a new and highly efficient approach to the construction of a physical map of human chromosome 11q.

Chromosomes, Human, Pair 11↗
PubMed2003

Rapid assembly of molecular diversity via exploitation of isocyanide-based multi-component reactions.

Molecular diversity is the variability of physical properties between molecules, viewed in terms of molecular shape, polarity/charge, lipophilicity, polarizability and flexibility. Due to their widespread medicinal properties, natural products were one of the original sources of molecular diversity; however, new developments in the search for novel pharmacological agents over the last decade have focused on the preparation of chemical libraries as the source of new leads for drug discovery. A plethora of personal synthesizers and new automation technologies have emerged to help fuel the lead discovery engines of drug discovery organizations. Multistep solid-phase syntheses of diverse libraries in excess of 10,000 products can now be prepared via split-and-mix techniques. Simultaneously, a multitude of more efficient, diversity- or target-oriented solution-phase chemical methodologies have appeared in the chemical literature, enabling the relatively facile construction of successful lead generation libraries with low full-time equivalent input and little capital expenditure. Isocyanide-related multi-component reactions hold a pre-eminent position in this regard, and are finding increasing applications in the discovery process of new drugs and agrochemicals. This review is the authors' personal assessment of advances in the field over the last two years (2002 to 2003), with little emphasis placed on highly mechanistic details.

Combinatorial Chemistry Techniques↗
PubMed2001

Sequence and structure of the mouse gene for RPE65.

PURPOSE: To determine the genomic organization of the mouse gene for the retinal pigment epithelium (RPE) specific protein RPE65. METHODS: A genomic clone containing the entire Rpe65 gene was isolated from a mouse genomic P1 library. Fragments of this clone were subcloned and sequenced by automated fluorescent dideoxy DNA sequencing and analyzed. Direct sequencing of PCR amplification products was used to complete the structure. Primer extension analysis was used to determine the transcription start site. RESULTS: Southern hybridization of restriction digests of mouse genomic DNA reveals a likely single autosomal gene for Rpe65 with no evidence of pseudogenes. Sequence analysis of the mouse P1 clone for Rpe65 and fragments thereof reveals 14 exons distributed over 27 kbp. The transcription start site is located 57 bp upstream of the initiation codon. The protein encoded by the mouse Rpe65 gene is highly conserved when compared with RPE65s from other species. CONCLUSIONS: RPE65 is a highly conserved protein and it appears that the genes for the mouse and human RPE65s, at least, are also conserved in overall structure.

Amino Acid Sequence↗
PubMed2001

Full-length cDNAs: more than just reaching the ends.

The development of functional genomic resources is essential to understand and utilize information generated from genome sequencing projects. Central to the development of this technology is the creation of high-quality cDNA resources and improved technologies for analyzing coding and noncoding mRNA sequences. The isolation and mapping of cDNAs is an entrée to characterizing the information that is of significant biological relevance in the genome of an organism. However, a bottleneck is often encountered when attempting to bring to full-length (or at least full-coding) a number of incomplete cDNAs in parallel, since this involves the nonsystematic, time consuming, and labor-intensive iterative screening of a number of cDNA libraries of variable quality and/or directed strategies to process individual clones (e.g., 5' rapid amplification of cDNA ends). Here, we review the current state of the art in cDNA library generation, as well as present an analysis of the different steps involved in cDNA library generation.

Automation↗
PubMed2003

Automated Parallel Oocyte Electrophysiology Test station (POETs): a screening platform for identification of ligand-gated ion channel modulators.

Ligand-gated ion channels (LGICs) play important roles in the regulation of cellular function and signaling and serve as excellent drug targets. However, fast desensitization of most LGICs limits the choice of reliable methods to identify agonists, antagonists, and/or modulators in a high throughput manner. In this study, automated Parallel Oocyte Electrophysiology Test station (POETs) was used to screen a directed compound library against a rapidly desensitizing LGIC and to characterize further the pharmacological properties of the hits. POETs allows up to six two-electrode voltage-clamp experiments to be performed in parallel by automatically loading of the oocytes into flowcells, assessing individual oocyte behavior prior to initiating experiments. Oocytes injected with cRNA were transferred from a chilled 96-well plate into flowcells by the instrument, where they were impaled under software control by two independent electrodes. Expression was tested by measuring current responses to rapid application of agonists. Compounds, prepared in a 96-well format, were tested for effects by coapplication with agonist at a single concentration of 30 microM over 2 s. After compound application, oocytes were washed for a minimum of 30 s, and used repeatedly if the test compounds had no significant effect on the control response. Typical throughput could reach approximately 14 plates/day depending on the protocol. Pilot library screening revealed a hit rate of 0.06%, with active compounds having IC(50) values of 4-40 microM. Hits were also confirmed in native neurons using patch-clamp techniques. We conclude that automated POETs serves as a suitable platform for screening and expedient identification of LGIC modulators.

Algorithms↗
PubMed2006

Development of assays for nuclear receptor modulators using fluorescently tagged proteins.

This chapter describes a method for designing cell-based assays to screen for nuclear receptor modulators. The basic strategy consists in following the movement of the receptors from the cytoplasm into the nucleus in response to ligand binding or analogous activating events. The receptors are tagged with green fluorescent protein for automated, fluorescent detection. In the case of constitutively nuclear receptors, they are engineered for cytoplasmic retention in the absence of an activating signal by fusing them to specific regions of the glucocorticoid receptor, which is found predominantly in the cytoplasm of cultured cells. The resulting chimeras respond to ligands or receptor modulators by translocating into the nucleus. This movement is monitored easily by automated fluorescent microscopy and serves as the basis for screening libraries. Finally, secondary assays built into the cell system can differentiate between modulators that stimulate, inhibit, or do not affect the transcriptional activity of the receptor under study. This approach has been validated for both the estrogen receptor and the retinoic acid receptor and should be applicable to any member of the superfamily, facilitating the identification of new ligands and selective receptor modulators.

Amino Acid Sequence↗
PubMedDate not supplied

Automated high-throughput synthesis of artificial glycopeptides. Small-molecule probes for chemical glycobiology.

A fully automated method for the synthesis of artificial glycopeptides having two (similar or different) carbon-linked glycosyl moieties on a dipeptide scaffold has been developed. By use of this approach that combines the diversity of peptide/pseudopeptide and glycosides, different glycoside moieties can be incorporated onto the peptide/pseudopeptide backbone in a highly controlled manner. The approach utilizes a stepwise reductive amination with glycoside aldehyde derivatives (model 1) or (ii) glycoside reductive amination followed by glycoside amide bond formation (model 2). Further, an automated method has been utilized in the high-throughput library synthesis of 4 x 96 artificial glycopeptides. These libraries were tested as chemical probes/inhibitors of enzyme systems that convert a glucose moiety into rhamnose prior to incorporation of the rhamnose unit and the conversion of UDP-galactopyranose to UDP-galactofuranose via UDP-galactopyranose mutase enzyme during the biosynthesis of the mycobacterium cell wall.

Combinatorial Chemistry Techniques↗
PubMed2004

Collaborative design for automated DNA storage that allows for rapid, accurate, large-scale studies.

Genomics Collaborative, Inc., a division of Sera Care Life Sciences, Inc. (Cambridge, MA), is among the first commercial entities in the world to enable genetic research on an industrial scale via its Large Scale Global Repository, a biobank of human specimens collected for research purposes. With the demand for large-scale DNA studies increasing, decisions about the strategic direction of sample storage and collection must be made to create a sound plan to support continued demands for drug discovery. Reported here is the approach used by Genomics Collaborative to automate its DNA processing, storage, and retrieval.

Automation↗
PubMed2003

Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors.

With the increasing number of eukaryotic genomes available, high-throughput automated tools for identification of regulatory DNA sequences are becoming increasingly feasible. Several computational approaches for the prediction of regulatory elements were recently developed. Here we combine the prediction of clusters of binding sites for transcription factors with context information taken from genome annotations. Target Explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at http://trantor.bioc.columbia.edu/Target_Explorer/

Animals↗
PubMed2006

Synthesis of metallothionein-mimic decapeptides with heavy atom signaling properties.

The automated parallel solid-phase synthesis of a 17-member library of metallothionein-mimic decapeptides carrying a Lariat ether group is described. The peptides were synthesized in good yield and the identity and quality of each product were performed by mass spectrometry and IR. Subsequently, in the presence of europium(III) ions as fluorescent reporter, each compound was screened, both attached to the resin and cleaved off, for their sensing behavior towards metal ions (Cd(2+),Hg(2+), Cu(2+), Mg(2+) and Ca(2+)) using fluorimetric techniques. Several of these Cys-enriched synthetic peptides showed surprisingly low detection limits for Cd(2+) and Hg(2+). The analytical potential of these metallothionein-mimic decapeptides as metal ion recognition materials for sensor development is outlined. Finally, the sensing response mechanism, based on an energy transfer process and a metal ion allosteric interaction, is proposed.

Allosteric Site↗
PubMed1997

[An entire rain forest can be screened at pharmaceutical industry's laboratories].

The pharmaceutical industry has long been heavily reliant on natural products, and today more than half of the twenty best-selling pharmaceuticals are derived from natural sources. Hitherto sample collection from fauna and flora has been based on an ethnobotanical approach involving traditional healers and oral histories of indigenous peoples as sources of information on folk uses of plants and organisms. In the future, however, random sampling combined with automated high-throughput screening (HTS) may come to the forefront in drug design, enabling extensive libraries of active compounds to be built up, and rendering local knowledge largely irrelevant. New technological advances in chemistry, molecular biology and data processing are combined in automated systems whereby HTS, based on bioassay-guided fractionation procedures, is used to isolate active compounds, and enabling the chemical structure of isolated compounds to be determined within 24 hours. The combination of the speed of HTS, and a remarkable decrease in the amount of sample required for the isolation and structure determination of natural compounds, has improved our ability to find unique natural products for drug development. Moreover, it has already been demonstrated that, owing to the relatively minute amounts of material required for HTS, this random sampling approach to bioprospecting for the purposes of drug will benefit efforts to conserve such sensitive biosystems as the rain forests and marine ecosystems. Thus, this technology would seem to be more compatible with the needs of modern drug design in the pharmaceutical industry that the ethnobotanical approach.

Drug Industry↗
PubMed2003

Dereplication of Streptomyces soil isolates and detection of specific biosynthetic genes using an automated ribotyping instrument.

The discrimination of distinct cultures among morphologically similar Streptomyces soil isolates (dereplication) and the detection of specific biosynthetic pathways in these strains are important steps in the selection of microorganisms to include in a natural products library. We have developed methods for analysis of actinomycetes using the RiboPrinter microbial characterization system, an automated instrument that performs ribotyping on bacterial samples. To evaluate our dereplication method, 26 Streptomyces isolates, obtained from soil samples collected in Maui, Hawaii, were ribotyped and compared with each other, using the RiboPrinter. The strains were also compared by 16S rDNA sequence analysis, MIDI fatty acid analysis, and LC-MS profiling of fermentation extracts. The RiboPrinter was able to identify closely related isolates and to discriminate between morphologically similar isolates with unique genetic, fatty acid and fermentation profiles. For the detection of biosynthetic genes, a 1,006-bp probe containing a portion of an adenylation domain of a non-ribosomal peptide synthetase (NRPS) was employed. Using this alternate probe in place of the standard ribosomal probe, the RiboPrinter was able to detect NRPS genes in several strains of Streptomyces. These results demonstrate that the RiboPrinter has multiple applications in a natural products research program.

Biotechnology↗
PubMed2004

Application of a Medical Text Indexer to an online dermatology atlas.

Clinical dermatology cases are presented as images and semi-structured text describing skin lesions and their relationships to disease. Metadata assignment to such cases is hampered by lack of a standardized dermatology vocabulary and facilitated methods for indexing legacy collections. In this pilot study descriptive clinical text from Dermatlas, a Web-based repository of dermatology cases, was indexed to Medical Subject Heading (MeSH) terms using the National Library of Medicine's Medical Text Indexer (MTI). The MTI is an automated text processing system that derives ranked lists of MeSH terms to describe the content of medical journal citations using knowledge from the Unified Medical Language System (UMLS) and from MEDLINE. For a representative, random sample of 50 Dermatlas cases, the MTI frequently derived MeSH indexing terms that matched expert-assigned terms for Diagnoses (88%), Lesion Types (72%), and Patient Characteristics (Gender and Age Groups, 62% and 84% respectively). This pilot demonstrates the potential for extending the MTI to automate indexing of clinical case presentations and for using MeSH to describe aspects of clinical dermatology.

Abstracting and Indexing↗