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PubMed1996

Affinity-based screening of combinatorial libraries using automated, serial-column chromatography.

We have developed an automated serial chromatographic technique for screening a library of compounds based upon their relative affinity for a target molecule. A "target" column containing the immobilized target molecule is set in tandem with a reversed-phase column. A combinatorial peptide library is injected onto the target column. The target-bound peptides are eluted from the first column and transferred automatically to the reversed-phase column. The target-specific peptide peaks from the reversed-phase column are identified and sequenced. Using a monoclonal antibody (3E-7) against beta-endorphin as a target, we selected a single peptide with sequence YGGFL from approximately 5800 peptides present in a combinatorial library. We demonstrated the applicability of the technology towards selection of peptides with predetermined affinity for bacterial lipopolysaccharide (LPS, endotoxin). We expect that this technology will have broad applications for high throughout screening of chemical libraries or natural product extracts.

Amino Acid Sequence↗
PubMed2005

Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series.

We outline an approach to simultaneously assess multilevel microbial diversity patterns utilizing 16S-ITS rDNA clone libraries coupled with automated ribosomal intergenic spacer analysis (ARISA). Sequence data from 512 clones allowed estimation of ARISA fragment lengths associated with bacteria in a coastal marine environment. We matched 92% of ARISA peaks (each comprising >1% total amplified product) with corresponding lengths from clone libraries. These peaks with putative identification accounted for an average of 83% of total amplified community DNA. At 16S rDNA similarities <98%, most taxa displayed differences in ARISA fragment lengths >10 bp, readily detectable and suggesting ARISA resolution is near the 'species' level. Prochlorococcus abundance profiles from ARISA were strongly correlated (r2=0.86) to Prochlorococcus cell counts, indicating ARISA data are roughly proportional to actual cell abundance within a defined taxon. Analysis of ARISA profiles for 42 months elucidated patterns of microbial presence and abundance providing insights into community shifts and ecological niches for specific organisms, including a coupling of ecological patterns for taxa within the Prochlorococcus, the Gamma Proteobacteria and Actinobacteria. Clade-specific ARISA protocols were developed for the SAR11 and marine cyanobacteria to resolve ambiguous identifications and to perform focused studies. 16S-ITS data allowed high-resolution identification of organisms by ITS sequence analysis, and examination of microdiversity.

Automation↗
PubMed1987

Cost considerations in automating the library.

The purchase price of a computer and its software is but a part of the cost of any automated system. There are many additional costs, including one-time costs of terminals, printers, multiplexors, microcomputers, consultants, workstations and retrospective conversion, and ongoing costs of maintenance and maintenance contracts for the equipment and software, telecommunications, and supplies. This paper examines those costs in an effort to produce a more realistic picture of an automated system.

Catalogs, Library↗
PubMed1987

Automating Veterans Administration libraries: I. National planning and development.

The Veterans Administration Library Network (VALNET) needed an automated library system that could interface with the agency's national automation activities. The Library Special Interest Users Group was established to oversee the selection of appropriate automated systems. The Massachusetts General Hospital Utility Multi-Programming System (MUMPS) computer language and VA FILEMAN, a database management system, are being used to create new library software, which will be in the public domain.

Computer Communication Networks↗
PubMed2004

A framework for a distributed, hybrid, multiple-ontology clinical-guideline library, and automated guideline-support tools.

Clinical guidelines are a major tool in improving the quality of medical care. However, most guidelines are in free text, not in a formal, executable format, and are not easily accessible to clinicians at the point of care. We introduce a Web-based, modular, distributed architecture, the Digital Electronic Guideline Library (DeGeL), which facilitates gradual conversion of clinical guidelines from text to a formal representation in chosen target guideline ontology. The architecture supports guideline classification, semantic markup, context-sensitive search, browsing, run-time application, and retrospective quality assessment. The DeGeL hybrid meta-ontology includes elements common to all guideline ontologies, such as semantic classification and domain knowledge; it also includes four content-representation formats: free text, semi-structured text, semi-formal representation, and a formal representation. These formats support increasingly sophisticated computational tasks. The DeGeL tools for support of guideline-based care operate, at some level, on all guideline ontologies. We have demonstrated the feasibility of the architecture and the tools for several guideline ontologies, including Asbru and GEM.

Computer Communication Networks↗
PubMed2001

Toxicological screening of urine for drugs by liquid chromatography/time-of-flight mass spectrometry with automated target library search based on elemental formulas.

The present study describes a novel approach for utilizing liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS) in qualitative screening analysis. An LC/TOFMS method was developed for screening toxicologically relevant substances in urine samples. After solid phase extraction and LC separation, the method included full spectrum acquisition followed by automatic internal calibration, searching against a target library, and reporting positive identifications. The target library, containing 433 toxicologically relevant substances in the mass range of 105-734 Da, was created simply by entering the elemental formulas of substances into the instrument software for the calculation of their respective monoisotopic masses. In addition to parent drugs, the library contained selected urinary drug metabolites, based on their structures available in the literature. Identification was based on the exact masses of the compounds. The LC/TOFMS method provided 5-10 ppm mass accuracy for a majority of identified compounds in authentic urine samples. Compared with established thin-layer and gas chromatographic methods, the LC/TOFMS method produced similar findings in urine with the additional advantage of metabolite identification without actual reference substances.

Calibration↗
PubMed1988

Building bridges: LIS-IAIMS-BioSYNTHESIS.

Recent progress in library automation and networking is redefining the library's traditional role. The Georgetown University Medical Center Library, developer of the Library Information System (LIS), has been involved in automation for nearly a decade, and was one of the first institutions to receive an NLMIAMS grant. The two projects have evolved together. New LIS modules, such as Document Delivery and the ALERTS/CURRENT CONTENTS Search System, have been designed in a reciprocal LIS/IAIMS environment. BioSYNTHESIS, a current IAIMS research project, is a prototype information tool for tomorrow.

Computer Systems↗
PubMed1976

Automation--planning to implementation; the problems en route.

Once the major decision to automate library processes is made, there are a variety of problems which may be encountered before the planned system becomes operational. These include problems of personnel, budget, procurement of adjunct services, institutional priorities, and manufacturing uncertainties. Actual and potential difficulties are discussed.

Automation↗
PubMed1983

Implementation of the Integrated Library System: University of Maryland Health Sciences Library.

The Health Sciences Library, University of Maryland, has implemented the Integrated Library System (ILS), a minicomputer-based library automation system developed by the Lister Hill National Center for Biomedical Communications, National Library of Medicine. The process of moving a library from a manual to a computerized system required comprehensive planning and strong commitment by the staff. Implementation activities included hardware and software modification, conversion of manual files, staff training, and system publicity. ILS implementation resulted in major changes in procedures in the circulation, reference, and cataloging departments.

Computers↗
PubMed2006

High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell.

BACKGROUND: The field of plasmid-based functional proteomics requires the rapid assay of proteins expressed from plasmid libraries. Automation is essential since large sets of mutant open reading frames are being cloned for evaluation. To date no integrated automated platform is available to carry out the entire process including production of plasmid libraries, expression of cloned genes, and functional testing of expressed proteins. RESULTS: We used a functional proteomic assay in a multiplexed setting on an integrated plasmid-based robotic workcell for high-throughput screening of mutants of cellulase F, an endoglucanase from the anaerobic fungus Orpinomyces PC-2. This allowed us to identify plasmids containing optimized clones expressing mutants with improved activity at lower pH. A plasmid library of mutagenized clones of the celF gene with targeted variations in the last four codons was constructed by site-directed PCR mutagenesis and transformed into Escherichia coli. A robotic picker integrated into the workcell was used to inoculate medium in a 96-well deep well plate, combining the transformants into a multiplexed set in each well, and the plate was incubated on the workcell. Plasmids were prepared from the multiplexed culture on the liquid handler component of the workcell and used for in vitro transcription/translation. The multiplexed expressed recombinant proteins were screened for improved activity and stability in an azo-carboxymethylcellulose plate assay. The multiplexed wells containing mutants with improved activity were identified and linked back to the corresponding multiplexed cultures stored in glycerol. Spread plates were prepared from the glycerol stocks and the workcell was used to pick single colonies from the spread plates, prepare plasmid, produce recombinant protein, and assay for activity. The screening assay and subsequent deconvolution of the multiplexed wells resulted in identification of improved CelF mutants and corresponding optimized clones in expression-ready plasmids. CONCLUSION: The multiplex method using an integrated automated platform for high-throughput screening in a functional proteomic assay allows rapid identification of plasmids containing optimized clones ready for use in subsequent applications including transformations to produce improved strains or cell lines.

Journal Article↗
PubMed1999

Digital information evolution: the AIDS Library experience.

The AIDS Library evolved out of consumer health activism in response to the need for the latest HIV information, materials, and technology. In 1998, staff implemented a microcomputer-based integrated automated library system with Web publishing capability to link catalogs, databases of Philadelphia regional services, online publications, and fact sheets. The Web site, , became "live" December 1, 1998. History leading to its development and future plans are presented.

Acquired Immunodeficiency Syndrome↗
PubMed1983

Integrated library systems.

The development of integrated library systems is discussed. The four major discussion points are (1) initial efforts; (2) network resources; (3) minicomputer-based systems; and (4) beyond library automation. Four existing systems are cited as examples of current systems.

Computers↗
PubMed1991

The impact of economic issues on Nigerian health sciences libraries.

Economic issues are among the most important factors affecting health sciences libraries in Nigeria. These issues are influenced by the political, cultural, geographic, and demographic characteristics of the country. Significant economic issues are the dependence of the national economy on a single commodity, large foreign debt and spiraling inflation, stringent foreign exchange control measures, and inadequate realization by authorities of the role and importance of health sciences libraries. With shrinking budgets, resources, and staff, health sciences libraries can neither grow nor afford library automation. Health sciences librarians must take initiatives for cooperative activities to increase and make the most of resources, pursue nontraditional methods of fund-raising, educate authorities about the role and importance of libraries, and develop and implement a plan for the development and growth of health sciences libraries in the country.

Financing, Government↗
PubMed1982

Automation of internal library operations in academic health sciences libraries: a state of the art report.

A survey of automated records management in the United States and Canada was developed to identify existing on-line library systems and technical expertise. Follow-up interviews were conducted with ten libraries. Tables compare the features and availability of four main frame and four minicomputer systems. Results showed: a trend toward vendor-supplied systems; little coordination of efforts among schools; current system developments generally on a universitywide basis; and the importance of having the cooperation of campus computer facilities to the success of automation efforts.

Automation↗
PubMed2007

Spot the match - wildlife photo-identification using information theory.

BACKGROUND: Effective approaches for the management and conservation of wildlife populations require a sound knowledge of population demographics, and this is often only possible through mark-recapture studies. We applied an automated spot-recognition program (I3S) for matching natural markings of wildlife that is based on a novel information-theoretic approach to incorporate matching uncertainty. Using a photo-identification database of whale sharks (Rhincodon typus) as an example case, the information criterion (IC) algorithm we developed resulted in a parsimonious ranking of potential matches of individuals in an image library. Automated matches were compared to manual-matching results to test the performance of the software and algorithm. RESULTS: Validation of matched and non-matched images provided a threshold IC weight (approximately 0.2) below which match certainty was not assured. Most images tested were assigned correctly; however, scores for the by-eye comparison were lower than expected, possibly due to the low sample size. The effect of increasing horizontal angle of sharks in images reduced matching likelihood considerably. There was a negative linear relationship between the number of matching spot pairs and matching score, but this relationship disappeared when using the IC algorithm. CONCLUSION: The software and use of easily applied information-theoretic scores of match parsimony provide a reliable and freely available method for individual identification of wildlife, with wide applications and the potential to improve mark-recapture studies without resorting to invasive marking techniques.

Journal Article↗
PubMed1999

A simple comparison of mass spectral search results and implications for environmental screening analyses

A simple assessment of the ability of environmental laboratories to perform automated library searching procedures on mass spectra of unknown pollutants was conducted. In this assessment, 10 laboratories analyzed a hexane solution containing eight organic chemicals using gas chromatography/mass spectrometry and searched their acquired mass spectral data against mass spectral reference libraries. The search results were used to evaluate the similarity of the lists of tentative identifications (TIDs) among the laboratories and to compare the observed searching success to the searching success reported in the literature using high-quality mass spectral data. A high degree of similarity was observed among the lists of TIDs reported by the laboratories for each chemical. The searching success observed in this study was slightly lower than that reported in the literature based on higher-quality mass spectral data. This simple comparison suggests that laboratories performing routine environmental analyses can successfully perform automated searching procedures for unknown sample components, and that the mass spectral searching component of analytical methods designed to screen for unknown organic pollutants should be successful, i.e., obtain similar and reproducible results among laboratories.

Journal Article↗
PubMed2001

Combinatorial chemistry toward understanding the function(s) of carbohydrates and carbohydrate conjugates.

Combinatorial chemistry has contributed significantly to understanding the structure-function relationships of biologically important molecules such as proteins and nucleic acids. However, carbohydrates and carbohydrate conjugates, which have been identified as key modulators of several biological functions have not enjoyed the same measure of success. The complexity and synthetic challenges of carbohydrate conjugates have resulted in a number of conceptual approaches to rapidly access sufficient quantities of these biomolecules. This article summarizes these combinatorial approaches and also highlights fully automated library synthesis of artificial glycopeptides with the goals of understanding their biological roles.

Carbohydrate Conformation↗