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At least 469 records · Page 26Linked to original sources
PubMed2004

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.

MOTIVATION: Several protein function prediction methods employ structural features captured in three-dimensional (3D) descriptors of biologically relevant sites. These methods are successful when applied to high-resolution structures, but their detection ability in lower resolution predicted structures has only been tested for a few cases. RESULTS: A method that automatically generates a library of 3D functional descriptors for the structure-based prediction of enzyme active sites (automated functional templates, 593 in total for 162 different enzymes), based on functional and structural information automatically extracted from public databases, has been developed and evaluated using decoy structures. The applicability to predicted structures was investigated by analyzing decoys of varying quality, derived from enzyme native structures. For 35% of decoy structures, our method identifies the active site in models having 3-4 A coordinate root mean square deviation from the native structure, a quality that is reachable using state of the art protein structure prediction algorithms. AVAILABILITY: See http://www.bioinformatics.buffalo.edu/resources/aft/

Algorithms↗
PubMed1999

An automated sample preparation system for large-scale DNA sequencing.

Recent advances in DNA sequencing technologies, both in the form of high lane-density gels and automated capillary systems, will lead to an increased requirement for sample preparation systems that operate at low cost and high throughput. As part of the development of a fully automated sequencing system, we have developed an automated subsystem capable of producing 10,000 sequence-ready ssDNA templates per day from libraries of M13 plaques at a cost of $0.29 per sample. This Front End has been in high throughput operation since June, 1997 and has produced > 400,000 high-quality DNA templates.

DNA↗
PubMed2006

Development of goose- and duck-specific DNA markers to determine sources of Escherichia coli in waterways.

The contamination of waterways with fecal material is a persistent threat to public health. Identification of the sources of fecal contamination is a vital component for abatement strategies and for determination of total maximum daily loads. While phenotypic and genotypic techniques have been used to determine potential sources of fecal bacteria in surface waters, most methods require construction of large known-source libraries, and they often fail to adequately differentiate among environmental isolates originating from different animal sources. In this study, we used pooled genomic tester and driver DNAs in suppression subtractive hybridizations to enrich for host source-specific DNA markers for Escherichia coli originating from locally isolated geese. Seven markers were identified. When used as probes in colony hybridization studies, the combined marker DNAs identified 76% of the goose isolates tested and cross-hybridized, on average, with 5% of the human E. coli strains and with less than 10% of the strains obtained from other animal hosts. In addition, the combined probes identified 73% of the duck isolates examined, suggesting that they may be useful for determining the contribution of waterfowl to fecal contamination. However, the hybridization probes reacted mainly with E. coli isolates obtained from geese in the upper midwestern United States, indicating that there is regional specificity of the markers identified. Coupled with high-throughput, automated macro- and microarray screening, these markers may provide a quantitative, cost-effective, and accurate library-independent method for determining the sources of genetically diverse E. coli strains for use in source-tracking studies. However, future efforts to generate DNA markers specific for E. coli must include isolates obtained from geographically diverse animal hosts.

Animals↗
PubMedDate not supplied

Electronic health record meets digital library: a new environment for achieving an old goal.

Linking the electronic health record to the digital library is a Web-era reformulation of the long-standing informatics goal of seamless integration of automated clinical data and relevant knowledge-based information to support informed decisions. The spread of the Internet, the development of the World Wide Web, and converging format standards for electronic health data and digital publications make effective linking increasingly feasible. Some existing systems link electronic health data and knowledge-based information in limited settings or limited ways. Yet many challenging informatics research problems remain to be solved before flexible and seamless linking becomes a reality and before systems become capable of delivering the specific piece of information needed at the time and place a decision must be made. Connecting the electronic health record to the digital library also requires positive resolution of important policy issues, including health data privacy, government encouragement of high-speed communications, electronic intellectual property rights, and standards for health data and for digital libraries. Both the research problems and the policy issues should be important priorities for the field of medical informatics.

Internet↗
PubMed1999

Analyses of compound libraries obtained by high-throughput parallel synthesis: strategy of quality control by high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance techniques.

The growing interest in combinatorial chemistry has led to a new source of compounds from which a large number of leads has emerged over recent years. Parallel synthesis, in particular, allows a quick production of a wide number of individual compounds. A rapid analytical control is needed to determine their quality. A strategy using automated, fast reversed-phase C18 high-performance liquid chromatography with diode-array detection (LC-DAD-MS) followed by atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) and NMR has been developed for their characterisation and purity control. Complementary NMR analyses are done on selected compounds to provide a better structural characterisation of the expected compounds and their potential side-products. Validated libraries are then registered in ISIS databases using automated procedures.

Chemistry, Pharmaceutical↗
PubMed1995

Molecular cloning of a phosphoinositide-specific phospholipase C from catfish olfactory rosettes.

A 2.7 kb clone encoding the partial (about 66%) sequence of a phosphoinositide-specific phospholipase C (PLC) was isolated from a cDNA library constructed from channel catfish (Ictalurus punctatus) olfactory rosettes. The clone, designated 30c7, was completely sequenced by automated DNA sequencing and was found to share significant homology with rat and bovine PLCs of the delta 1 isotype. In situ hybridization showed that 30c7 transcripts were expressed in a small subpopulation of olfactory neurons, as well as in other cell types in the olfactory epithelium. Polymerase chain reaction (PCR) analysis indicated that the enzyme was also expressed in several additional tissues, including brain, gill, heart, liver and skeletal muscle. These results suggest that the PLC encoded by clone 30c7 is expressed in several tissues and therefore may have a role in mediating transduction events in diverse tissues as well as in a small group of olfactory neurons.

Amino Acid Sequence↗
PubMedDate not supplied

Prediction of HPLC conditions using QSPR techniques: an effective tool to improve combinatorial library design.

The purification and characterization of compounds resulting from parallel synthesis or combinatorial chemistry has not yet been optimized to operate as a completely automated high-throughput process. Liquid chromatography/mass spectroscopy (LC/MS) is most commonly employed to carry out the characterization and identification of combinatorial compounds. This desired level of automation can only be accomplished if the separation conditions for every compound in the combinatorial array are known prior to the analysis. This study presents a quantitative structure retention relationship (QSRR) approach to predict the retention time of structurally diverse solutes under 75 different LC/MS conditions. Sixty-two compounds were analyzed using 15 commonly used HPLC columns under 5 different gradient conditions. The solute retention time was used as the dependent variable, and more than 1000 molecular descriptors were calculated for this compound set to generate QSRR models. After the elimination of highly correlated variables and those with zero variance, two different genetic algorithms were applied to identify the most significant descriptors. Following the variable selection, the identified descriptors were used to create QSRR models for each separation condition. The calculated stepwise multiple linear regression models have been proven to be statistically significant and highly predictive, with an average coefficient of determination (R2) of 0.86, an average cross-validated r2 of 0.62, r2 = 0.76, and an average F value of 27.29. The QSRR models can be used to design "analysis-friendly" library purification plates, in which compounds are arranged on the basis of their predicted separation condition and can also be used during the library design phase to flag compounds not amenable to the separation methods in use.

Journal Article↗
PubMed1996

Comparative assessment of shockable ECG rhythm detection algorithms in automated external defibrillators.

The sensitivity and specificity to ventricular fibrillation (VF) and ventricular tachycardia (VT), classified as requiring immediate DC shock, of four automated external defibrillators (AEDs) and three advisory defibrillators were assessed using the Department of Health Arrhythmia library. This library collected mostly from patients in hospital, includes a wide variety of ECG rhythms including many with additional noise and interference artefact. The library comprised 278 16-s rhythms, 59 of which were VF, 36 were VT requiring cardioversion and 183 were deemed non-shockable. Non-shockable rhythms included asystole, pacing, slow VT, idioventricular rhythms, sinus and atrial based rhythms, some of which contained ventricular ectopic activity of differing grades. For the AEDs, a positive result (indicating detection of a shockable rhythm) was recorded if charging started or was able to be started at any time during the 16 s of rhythm output and energy subsequently available for discharge. For the advisory defibrillators, a positive result was recorded if a 'shock advised' alert was issued at any time during output of the rhythm. The AEDs exhibited sensitivities to VF in the range 81-94%, and to VF plus shockable VT 64-73%, or 72-83% depending whether VT > 150 beats/min or > 180 beats/min is considered to be shockable. The specificities recorded were in the range 90-94% and 86-92%, respectively. All but one of the advisory defibrillators performed similarly. Excluding the artefact rhythms, specificities in the range 79-91% were obtained. All figures stated are at the lower limit of the 95% confidence interval.

Algorithms↗
PubMed2003

Biological mechanism profiling using an annotated compound library.

We present a method for testing many biological mechanisms in cellular assays using an annotated library of 2036 small organic molecules. This annotated compound library represents a large-scale collection of compounds with diverse, experimentally confirmed biological mechanisms and effects. We found that this chemical library is (1) more structurally diverse than conventional, commercially available libraries, (2) enriched in active compounds in a tumor cell viability assay, and (3) capable of generating hypotheses regarding biological mechanisms underlying cellular processes. We elucidated biological mechanisms relevant to the antiproliferative activity of 85 compounds from this library that were selected using a high-throughput cell viability screen. We developed a novel automated scoring system for identifying statistically enriched mechanisms among such a subset of compounds. This scoring system can identify both previously known and potentially novel antiproliferative mechanisms.

Cell Line, Tumor↗
PubMed2004

Characterization of complex hydrocarbons in cigarette smoke condensate by gas chromatography-mass spectrometry and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

Gas chromatography-mass spectrometry with electron ionization and positive-ion chemical ionization and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC x GC-TOF-MS) were applied for the characterization of the chemical composition of complex hydrocarbons in the non-polar neutral fraction of cigarette smoke condensates. Automated data processing by TOF-MS software combined with structured chromatograms and manual review of library hits were used to assign the components from GC x GC-TOF-MS analysis. The distributions of aliphatic hydrocarbons and aromatics were also investigated. Over 100 isoprenoid hydrocarbons were detected, including carotene degradation products, phytadiene isomers and carbocyclic diterpenoids. A total of 1800 hydrocarbons were tentatively identified, including aliphatic hydrocarbons, aromatics, and isoprenoid hydrocarbons. The identified hydrocarbons by GC x GC-TOF-MS were far more than those by GC-MS.

Gas Chromatography-Mass Spectrometry↗
PubMedDate not supplied

A novel frequency distribution selection method for efficient plate layout of a diverse combinatorial library.

A deterministic method (frequency distribution method) for selecting compounds from a partitioned virtual combinatorial library for efficient synthesis is presented here. The method is based on reagent frequency analysis and can be applied to any library of molecules distributed in any given partitioned chemical space (cluster, cell-based, etc.). Compound selection by reagent frequency distribution can produce a unique, diverse set of molecules that adequately represents the library while requiring the least amount of compounds to be synthesized and minimizing the number of different reagents that must be used. This method also provides a practical solution to the configuration of plate layout. Because the method essentially identifies "expensive" regions in the chemical space to synthesize for a desired diversity or similarity coverage, decisions concerning the necessity to synthesize these compounds can be addressed. Minimum compound generation and efficient plate layout results in savings both in time of synthesis and cost of materials. This method always results in a discrete solution, which can be used for any given library size as well as any combination of reagents and is also readily adaptable to robotic automation.

Journal Article↗
PubMed2004

History, evolution, and trends in compound management for high throughput screening.

Growth in compound library size with increasing levels of high throughput screening has resulted in the complementary development of automated hardware and software systems for compound management. The history of this technology from its emergence in the early 1990s, its current status, and future trends are all described. The perspective is primarily a personal one, based on the author's involvement with compound management from its outset to the present day.

Agrochemicals↗
PubMed2004

Efficient filtering methods for clustering cDNAs with spliced sequence alignment.

MOTIVATION: Clustering sequences of a full-length cDNA library into alternative splice form candidates is a very important problem. RESULTS: We developed a new efficient algorithm to cluster sequences of a full-length cDNA library into alternative splice form candidates. Current clustering algorithms for cDNAs tend to produce too many clusters containing incorrect splice form candidates. Our algorithm is based on a spliced sequence alignment algorithm that considers splice sites. The spliced sequence alignment algorithm is a variant of an ordinary dynamic programming algorithm, which requires O(nm) time for checking a pair of sequences where n and m are the lengths of the two sequences. Since the time bound is too large to perform all-pair comparison for a large set of sequences, we developed new techniques to reduce the computation time without affecting the accuracy of the output clusters. Our algorithm was applied to 21 076 mouse cDNA sequences of the FANTOM 1.10 database to examine its performance and accuracy. In these experiments, we achieved about 2-12-fold speedup against a method using only a traditional hash-based technique. Moreover, without using any information of the mouse genome sequence data or any gene data in public databases, we succeeded in listing 87-89% of all the clusters that biologists have annotated manually. AVAILABILITY: We provide a web service for cDNA clustering located at https://access.obigrid.org/ibm/cluspa/, for which registration for the OBIGrid (http://www.obigrid.org) is required.

Algorithms↗
PubMedDate not supplied

Efficiency of automated literature search mechanisms.

This article explores the efficiency of automated literature search techniques to facilitate literature accessibility. It presents three related studies using the National Library of Medicine ( NLM ) literature search on nurse practitioners (1980) as the point of reference. The studies investigate three questions: Is the search reproducible, does it locate the most important articles pertaining to nurse practitioner effectiveness, and can a system be developed to decide efficiently which articles in a voluminous search output should actually be obtained? Results indicate that the NLM search is reproducible but that it lists only a small proportion of available studies. Neither the NLM document nor a computer search using the parameters it cites located a high proportion of critically nominated studies. However, based upon classification of their titles, a workable system can be developed to identify those articles in a search output that are relevant and should be retrieved.

Bibliographies as Topic↗
PubMed1994

HUBNET: Wide Area Network utilization of Local Area Network medical reference and communication resources.

The State University of New York at Buffalo School of Medicine and Biomedical Sciences and its associated teaching sites have developed and partially implemented a regional Wide Area Network (WAN) in Buffalo and Western New York. The school wishes to use this WAN to deliver reference and communication resources to students, residents and faculty. The richest pool of easy to use reference and communication resources are PC software programs that are intended for individual workstations or at best, client-server, Local Area Network (LAN) implementation. HUBNET (Hospitals and University at Buffalo Library Resource Network), a project of the School of Medicine and the Library Consortium of Health Institutions in Buffalo offers integrated presentation of many such LAN resources over this regional WAN. The system crosses many institutional boundaries and reaches physically remote sites in a complex mix of information systems environments with few issues related to performance. The system design provides a level of ease of use that has brought many new users into active computer use while addressing integration into diverse information systems settings and networking environments.

Computer Communication Networks↗
PubMed1991

An automated method for DNA preparation from thousands of YAC clones.

We describe an automated method for the preparation of yeast genomic DNA capable of preparing thousands of DNAs in parallel from a YAC library. Briefly, the protocol involves four steps: (1) Yeast clones are grown in the wells of 96-well microtiter plates with filter (rather than plastic) well-bottoms, which are embedded in solid growth media; (2) These yeast cultures are resuspended and their concentrations determined by optical density measurement; (3) Equal numbers of cells from each well are embedded in low-melting temperature agarose blocks in fresh 96-well plates, again with filter bottoms; and (4) DNA is prepared in the agarose blocks by a protocol similar to that used for preparing DNA for pulsed-field gels, with the reagents being dialyzed through the (filter) bottoms of the microtiter plate. The DNA produced by this method is suitable for pulsed-field gel electrophoresis, for restriction enzyme digestion, and for the polymerase chain reaction (PCR). Using this protocol, we produced 3000 YAC strain DNAs in three weeks. This automated procedure should be extremely useful in many genomic mapping projects.

Blotting, Southern↗
PubMed1999

An improved nonisotopic test to screen a large series of new inhibitor molecules of poly(ADP-ribose) polymerase activity for therapeutic applications.

A reliable ELISA for screening large numbers of poly(ADP-ribose) polymerase (PARP) inhibitors is described. The test is based upon the drop in PARP activity estimated by the decrease in poly(ADP-ribose) synthesis in the presence of inhibitor. This ELISA is easy to perform, rapid, and specific. It is extremely sensitive because a clear inhibition of the total reaction could be visualized with molecules used in the nanomolar range. The assay uses no radioactivity, and automation is possible with robots for large-scale investigations. This test is of great interest for the screening of chemical libraries and the discovery of new inhibitors (and possibly activators) of PARP. Such molecules have important applications in all abnormal situations involving DNA damage and oxidative stress, such as cancer, autoimmunity, diabetes, myocardial dysfunctions, certain infections, aging, and radiation/chemical exposure.

Apoptosis↗
PubMed1986

A complete library of point substitution mutations in the glucocorticoid response element of mouse mammary tumor virus.

The glucocorticoid response element (GRE) of mouse mammary tumor virus (MMTV) was chemically synthesized as two complementary DNA strands bearing cohesive termini. During automated synthesis, random mutations were introduced into the DNA by "doping" each of the four nucleoside phosphoramidites (A, G, C, and T) with a low level of the other three. These preparations were annealed and cloned into an M13 phage vector to produce a library of GRE mutants. Mutations within the synthesized region were identified by sequencing phage isolates at random. All of the chemically distinct classes of transition and transversion mutations have been observed. Statistical considerations indicate that the library contains all of the possible 90 point substitution mutations within a 30-nucleotide mutagenic target. So far 88 of these substitutions have been isolated, 74 as single mutants. At least two of the three possible single mutants at each of the 30 positions have been identified.

Base Sequence↗