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PubMed2002

Tagging gene and protein names in biomedical text.

MOTIVATION: The MEDLINE database of biomedical abstracts contains scientific knowledge about thousands of interacting genes and proteins. Automated text processing can aid in the comprehension and synthesis of this valuable information. The fundamental task of identifying gene and protein names is a necessary first step towards making full use of the information encoded in biomedical text. This remains a challenging task due to the irregularities and ambiguities in gene and protein nomenclature. We propose to approach the detection of gene and protein names in scientific abstracts as part-of-speech tagging, the most basic form of linguistic corpus annotation. RESULTS: We present a method for tagging gene and protein names in biomedical text using a combination of statistical and knowledge-based strategies. This method incorporates automatically generated rules from a transformation-based part-of-speech tagger, and manually generated rules from morphological clues, low frequency trigrams, indicator terms, suffixes and part-of-speech information. Results of an experiment on a test corpus of 56K MEDLINE documents demonstrate that our method to extract gene and protein names can be applied to large sets of MEDLINE abstracts, without the need for special conditions or human experts to predetermine relevant subsets. AVAILABILITY: The programs are available on request from the authors.

Abbreviations as Topic↗
PubMed1996

Octamer-primed cycle sequencing: design of an optimized primer library.

This paper describes a novel method of primer walking using octamer oligonucleotides to prime DNA sequencing reactions. Octamer sequencing is compatible with isotopic and fluorescent sequencing chemistry, reaction conditions are optimized such that the samples can be processed in parallel, and the procedure has the potential to be automated. This strategy is faster than the traditional primer walking sequencing strategy, as the existence of a primer library allows immediate access to a primer for the next sequencing reaction, eliminating delays associated with designing and synthesizing gene-specific primers. The octamer library is comprised of optimized sequencing primers, such that octamer sequencing yields results equivalent to or better than traditional primer walking. This technology is more economical because gene-specific sequencing primers, the major cost in the reaction, are replaced by an optimized subset of frequently occurring octamers that are able to prime multiple reactions.

Anabaena↗
PubMed1994

The evolution of research library buildings.

The principles of research library building planning established in the late 1940s emphasized flexibility of design; interspersal of books and readers; collaboration between librarians and architects; and an increased role for the library in education. Planning a medical research library in today's electronic environment requires attention to these principles as well as dealing with new and emerging technologies; economic constrains; new modes of scholarly research and communication; and the convergence of library science and information services on the campus. The social role of the library and the celebration of the book are factors common to both generations.

Architecture↗
PubMed1991

Single cell assay with an automated capillary microinjection system.

An automated capillary microinjection system with computer controlled positioning of the cells and of the capillary, and its applications and advantages are described. About 1500 injections are possible in one hour, with high reproducibility. In cytoplasmic and nuclear injections more than 90% and 85% of the cells are successfully injected. Using FITC-Dextran at a concentration of 0.5% as a fluorescently labelled coinjection marker, 99% of the cells can be retrieved in culture medium even 48 hours after injection. The coordinates of the cells are stored in the computer and accuracy in statistical evaluation of experiments is improved in comparison to the manual techniques. Methods for preparation and handling of glass capillaries were developed resulting in reproducible form and significantly reduced clogging rate. The improved characteristics offered by this system are demonstrated in studies leading to the confirmation of existence of mRNA(s) inhibiting cell proliferation. Functional screening by cell injections of cDNA libraries and of size fractionated mRNA molecules can be performed efficiently with the automated microinjection system.

Animals↗
PubMed2002

Development of combinatorial chemistry methods for coatings: high-throughput screening of abrasion resistance of coatings libraries.

Design, validation, and implementation of an optical spectroscopic system for high-throughput analysis of combinatorially developed protective organic coatings are reported. Our approach replaces labor-intensive coating evaluation steps with an automated system that rapidly analyzes 8 x 6 arrays of coating elements that are discretely deposited on a single plastic substrate. Each coating element of the library is 10 mm in diameter and 2-5 microm thick. Performance of coatings is evaluated with respect to their resistance to wear abrasion because this parameter is one of the primary considerations in end-use applications. Upon testing, the coating materials undergo changes that are impossible to quantitatively predict using existing knowledge. Coatings are abraded using industry-accepted abrasion test methods at a single or multiple abrasion conditions followed by the high-throughput analysis of abrasion-induced light scatter. The developed automated system is optimized for the analysis of diffusively scattered light that corresponds to 0-30% haze. System precision of 0.1-2.5% relative standard deviation provides capability for the reliable ranking of coatings performance. Although the system was implemented for high-throughput screening of combinatorially developed organic protective coatings for automotive applications, it can be applied for a variety of other applications for which materials ranking can be achieved using optical spectroscopic tools.

Journal Article↗
PubMed2001

In vivo drug target discovery: identifying the best targets from the genome.

A vast number of genes of unknown function threaten to clog drug discovery pipelines. To develop therapeutic products from novel genomic targets, it will be necessary to correlate biology with gene sequence information. Industrialized mouse reverse genetics is being used to determine gene function in the context of mammalian physiology and to identify the best targets for drug development.

Animals↗
PubMed2001

Mass spectrometry innovations in drug discovery and development.

This review highlights the many roles mass spectrometry plays in the discovery and development of new therapeutics by both the pharmaceutical and the biotechnology industries. Innovations in mass spectrometer source design, improvements to mass accuracy, and implementation of computer-controlled automation have accelerated the purification and characterization of compounds derived from combinatorial libraries, as well as the throughput of pharmacokinetics studies. The use of accelerator mass spectrometry, chemical reaction interface-mass spectrometry and continuous flow-isotope ratio mass spectrometry are promising alternatives for conducting mass balance studies in man. To meet the technical challenges of proteomics, discovery groups in biotechnology companies have led the way to development of instruments with greater sensitivity and mass accuracy (e.g., MALDI-TOF, ESI-Q-TOF, Ion Trap), the miniaturization of separation techniques and ion sources (e.g., capillary HPLC and nanospray), and the utilization of bioinformatics. Affinity-based methods coupled to mass spectrometry are allowing rapid and selective identification of both synthetic and biological molecules. With decreasing instrument cost and size and increasing reliability, mass spectrometers are penetrating both the manufacturing and the quality control arenas. The next generation of technologies to simplify the investigation of the complex fate of novel pharmaceutical entities in vitro and in vivo will be chip-based approaches coupled with mass spectrometry.

Drug Design↗
PubMed1988

Cloning and expression in Escherichia coli of the gene for mouse tumor necrosis factor.

The mouse tumor necrosis factor (TNF) gene was isolated from a mouse genomic library. The entire sequence of the gene was determined using both an automated DNA sequencer with improved primer extension reaction conditions as well as the standard radioisotopic method. Comparison of the nucleotide sequence of the gene with that of mouse TNF cDNA showed that the mouse gene consists of four exons, like rabbit and human TNF genes. There is strong nucleotide sequence homology in the 5'-flanking region among the mouse, rabbit, and human TNF genes, suggesting that the mechanisms regulating TNF gene expression are highly conserved. Direct expression of mature mouse TNF was achieved using a plasmid constructed by site-directed mutagenesis. Purified mouse TNF produced in Escherichia coli showed cytotoxicity to mouse L cells.

Amino Acid Sequence↗
PubMed1996

A rapid method for detecting specific amplified PCR fragments in microtiter plates.

A simple method is presented to circumvent laborious and time consuming electrophoretic separations of specific PCR amplification products. Specific target DNA is amplified using nucleotides labelled with DIG-dUTP or biotin-dCTP. The labelled PCR products are separated from unincorporated nucleotides or oligonucleotides by using a positively charged DEAE cellulose matrix. Amplification products are visualized directly in the matrix using immunoenzymatic methods or streptavidin-conjugated enzymes. The detection process can be carried out within 2 h, allows the processing of large sample sizes and can potentially be automated.

DNA↗
PubMed2001

Combinatorial Heterogeneous Catalysis-A New Path in an Old Field.

Combinatorial catalysis is the systematic preparation, processing, and testing of large diversities of chemically and physically different materials libraries in a high-throughput fashion. It also embodies microfabrication, robotics, automation, instrumentation, computational chemistry, and large-scale information management (informatics), and as such carries the promise of a renaissance in catalytic reaction engineering. Significant progress has already been made in demonstrating the speed and economic advantage of combinatorial approaches by the discovery of superior catalytic materials in a matter of hours and days, as opposed to the months and years required using traditional methods. Combinatorial methods can also significantly contribute to our understanding of catalytic function by increasing our chances of discovering totally new and unexpected catalytic materials, and by expediting the recognition of trends and patterns of structure-activity relations, from which new catalytic materials can be designed more efficiently. Combinatorial catalysis undoubtedly will be the new paradigm of catalysis research as the industry faces increasing global competition and pressure for the development of environmentally friendly processes at a time when resources for research are diminishing.

Journal Article↗
PubMed1986

The formation of learning sets by the chinchilla in an auditory discrimination task.

The performance of 9 chinchillas (Chinchilla lanigera) in a completely computer-automated sound-discrimination experiment was observed using stimulus pairs from a library of 180 complex sounds. Each sound of a pair was 0.2-2.08 sec in duration, separated by an interval of 250 +/- 125 msec. A modified "go/no go" paradigm was used. Licking behavior at a water-delivery tube was occasioned by keeping Ss at about 85% of ad-lib weight by water deprivation. After habituation and blank-trials training stages, sound discrimination was required: If the sounds of a pair were identical, no response was required; if they were different, a fleeing response (crossing a mid-cage barrier) was required. Each problem set utilized a different sound pair, for a total of 90 problems. Therefore, Ss learned to perform general auditory discriminations, not sound-specific discriminations. The chinchillas quickly learned to respond, but not at a rate consistently higher than 75 %-correct. The results were compared to those of other studies of sensory discrimination in monkey and chinchilla. Suggestions were made for minor improvement of the paradigm for use in future sound-discrimination tasks.

Animals↗
PubMed2000

Molecular surveillance of European quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping.

Nosocomial isolates of Pseudomonas aeruginosa and Acinetobacter spp. exhibit high rates of resistance to antibiotics and are often multidrug resistant. In a previous study (D. Milatovic, A. Fluit, S. Brisse, J. Verhoef, and F. J. Schmitz, Antimicrob. Agents Chemother. 44:1102-1107, 2000), isolates of these species that were resistant to sitafloxacin, a new advanced-generation fluoroquinolone with a high potency and a broad spectrum of antimicrobial activity, were found in high proportion in 23 European hospitals. Here, we investigate the clonal diversity of the 155 P. aeruginosa and 145 Acinetobacter spp. sitafloxacin-resistant isolates from that study by automated ribotyping. Numerous ribogroups (sets of isolates with indistinguishable ribotypes) were found among isolates of P. aeruginosa (n = 34) and Acinetobacter spp. (n = 16), but the majority of the isolates belonged to a limited number of major ribogroups. Sitafloxacin-resistant isolates (MICs > 2 mg/liter, used as a provisional breakpoint) showed increased concomitant resistance to piperacillin, piperacillin-tazobactam, ceftriaxone, ceftazidime, amikacin, gentamicin, and imipenem. The major ribogroups were repeatedly found in isolates from several European hospitals; these isolates showed higher levels of resistance to gentamicin and imipenem, and some of them appeared to correspond to previously described multidrug-resistant international clones of P. aeruginosa (serotype O:12) and Acinetobacter baumannii (clones I and II). Automated ribotyping, when used in combination with more discriminatory typing methods, may be a convenient library typing system for monitoring future epidemiological dynamics of geographically widespread multidrug-resistant bacterial clones.

4-Quinolones↗
PubMed1999

A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases.

The discovery of various protein/receptor targets from genomic research is expanding rapidly. Along with the automation of organic synthesis and biochemical screening, this is bringing a major change in the whole field of drug discovery research. In the traditional drug discovery process, the industry tests compounds in the thousands. With automated synthesis, the number of compounds to be tested could be in the millions. This two-dimensional expansion will lead to a major demand for resources, unless the chemical libraries are made wisely. The objective of this work is to provide both quantitative and qualitative characterization of known drugs which will help to generate "drug-like" libraries. In this work we analyzed the Comprehensive Medicinal Chemistry (CMC) database and seven different subsets belonging to different classes of drug molecules. These include some central nervous system active drugs and cardiovascular, cancer, inflammation, and infection disease states. A quantitative characterization based on computed physicochemical property profiles such as log P, molar refractivity, molecular weight, and number of atoms as well as a qualitative characterization based on the occurrence of functional groups and important substructures are developed here. For the CMC database, the qualifying range (covering more than 80% of the compounds) of the calculated log P is between -0.4 and 5.6, with an average value of 2.52. For molecular weight, the qualifying range is between 160 and 480, with an average value of 357. For molar refractivity, the qualifying range is between 40 and 130, with an average value of 97. For the total number of atoms, the qualifying range is between 20 and 70, with an average value of 48. Benzene is by far the most abundant substructure in this drug database, slightly more abundant than all the heterocyclic rings combined. Nonaromatic heterocyclic rings are twice as abundant as the aromatic heterocycles. Tertiary aliphatic amines, alcoholic OH and carboxamides are the most abundant functional groups in the drug database. The effective range of physicochemical properties presented here can be used in the design of drug-like combinatorial libraries as well as in developing a more efficient corporate medicinal chemistry library.

Algorithms↗
PubMed1997

High throughput analysis and purification in support of automated parallel synthesis.

Rapid reverse-phase analytical and preparative HPLC methods have been developed for application to parallel synthesis libraries. Gradient methods, short columns, and high flow rates allow analysis of over 300 compounds per day on a single system, or purification of up to 200 compounds per day on a single preparative system. Hardware and software modifications allow continuous unattended use for maximum efficiency and throughput.

Automation↗
PubMed1983

Automated metabolic profiling analysis of urinary steroids by a gas chromatography mass spectrometry data system.

A computer system (MSSMET), using methylene unit retention indices for an off-line reverse library search analysis of selected ion chromatograms from gas-liquid chromatographic mass spectrometric data, has been applied for the qualitative and quantitative determination of daily variations in the excreted levels of urinary steroids of two individuals, using capillary column gas-liquid chromatography. Aliquots of 24 h urine collections and morning spot urine samples were examined. The daily excretion pattern of most of the major steroid metabolites was fairly consistent from day to day (i.e. 3 alpha-hydroxy-5 alpha-androstane-17-one, androsterone; 3 alpha-hydroxy-5 beta-androstane-17-one, etiocheolanolone; 3 alpha, 17 alpha, 21-trihydroxy-5 beta-pregnane-11,20-dione, THE; 3 alpha, 11 beta, 17 alpha, 21-tetrahydroxy-5 beta-pregnane-20-one, THF; 3 alpha, 11 beta, 17 alpha, 21-tetrahydroxy-5 alpha-pregnane-20-one; allo-THF; 3 alpha, 17 alpha, 20 alpha, 21-tetrahydroxy-5 beta-pregnane-11-one, cortolone; 3 alpha, 17 alpha, 20 beta, 21-tetrahydroxy-5 beta-pregnane-11-one, beta-cortolone; 5 beta-pregnane-3 alpha, 11 beta,17 alpha,20 alpha,21-pentol, cortol; 5 beta-pregnane-3 alpha, 11 beta, 17 alpha, 20 beta, 21-pentol, beta-cortol), while certain other steroid metabolites had a less consistent excretion pattern (3 beta-hydroxy-5-androstene-17-one, for example). Advantages and disadvantages of using capillary columns for the automated metabolic profile analysis of urinary steroids by reverse library search of selected mass chromatograms.

Adult↗