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At least 253 records · Page 14Linked to original sources
PubMed2004

Combinatorial codon-based amino acid substitutions.

Twenty Fmoc-protected trinucleotide phosphoramidites representing a complete set of codons for the natural amino acids were chemically synthesized for the first time. A pool of these reagents was incorporated into oligonucleotides at substoichiometric levels to generate two libraries of variants that randomly carry either few or many codon replacements on a region encoding nine amino acids of the bacterial enzyme TEM-1 beta-lactamase. Assembly of the libraries was performed in a completely automated mode through a simple modification of ordinary protocols. This technology eliminates codon redundancy, stop codons and enables complete exploration of sequence space for single, double and triple mutations throughout a protein region spanning several residues. Sequence analysis of many non-selected clones revealed a good incorporation of the trinucleotides, producing combinations of mutations quite different from those obtained using conventional degenerate oligonucleotides. Ceftazidime-selection experiments yielded several never before reported variants containing novel amino acid combinations in the beta-lactamase omega loop region.

Amino Acid Substitution↗
PubMed2006

Exact-mass library for pesticides using a molecular-feature database.

An automated molecular-feature database (MFD) consisting of the exact monoisotopic mass of 100 compounds, at least one exact mass product ion for each compound, and chromatographic retention time were used to identify pesticides in food and water samples. The MFD software compiles a list of accurate mass ions, excludes noise, and compares them with the monoisotopic exact masses in the database. The screening criteria consisted of +/-5 ppm accurate mass window, +/-0.2 min retention time window, and a minimum 1000 counts (signal-to-noise (S/N) ratio of approximately 10:1). The limit of detection for 100 tested compounds varied from <0.01 mg/kg for 72% of the compounds to <0.1 mg/kg for 95% of the compounds. The MFD search was useful for rapid screening and identification of pesticides in food and water, as shown in actual samples. The combined use of accurate mass and chromatographic retention time eliminated false positives in the automated analysis. The major weakness of the MFD is matrix interferences and loss of mass accuracy. Strengths of the MFD include rapid screening of 100 compounds at sensitive levels compared with a manual approach and the ease of use of the library for any accurate mass spectrometer instrumentation capable of routine sub-5-ppm mass accuracy.

Algorithms↗
PubMed2002

Automated screening procedure for high-throughput generation of antibody fragments.

In the emerging field of proteomics, there is an urgent need for catcher molecules such as antibodies for detecting the proteome or parts of the proteome in a microarray format. A suitable source for providing a large diversity of binders is obtained by combinatorial libraries, such as phage display libraries of single chain antibody fragments (scFv) or Fab fragments. To find novel binders from the n-CoDeR libraries with a high throughput, we have automated the screening process with robotics. The automated system is configured to screen tens of thousands of clones per day to target antigens in various formats, including peptides and soluble proteins, as well as cell-bound targets; thus, it is well designed to meet demands from the proteomics area.

Antigens↗
PubMed2002

High-throughput analysis of natural product compound libraries by parallel LC-MS evaporative light scattering detection.

The application of an 8-way fully automated parallel LC-MS-ELSD system to the analysis of a library of 96 structurally diverse natural products is described. A 10-min separation incorporating a universal gradient allowed elution of 86 of these 96 compounds, all of which were detected by positive or negative mode electrospray ionization in conjunction with ELSD. This method is demonstrated to be one of the most universal means of detection for polar, nonvolatile, thermally labile natural products. It also allows an 8-fold increase in throughput. The analysis and profiling of constituents present in a library derived from plant material of Sarcostemma hirtellum, in terms of their retention times and mass spectra, are shown. This rapid characterization of plant constituents in terms of compound libraries is important in searching for new biologically active compounds. As a high-throughput tool to support our natural product discovery program, this method has been successfully used to analyze a library of 36,000 partially purified fractions derived from plant materials.

Biological Factors↗
PubMed2002

Triage protein fold prediction.

We have constructed, in a completely automated fashion, a new structure template library for threading that represents 358 distinct SCOP folds where each model is mathematically represented as a Hidden Markov model (HMM). Because the large number of models in the library can potentially dilute the prediction measure, a new triage method for fold prediction is employed. In the first step of the triage method, the most probable structural class is predicted using a set of manually constructed, high-level, generalized structural HMMs that represent seven general protein structural classes: all-alpha, all-beta, alpha/beta, alpha+beta, irregular small metal-binding, transmembrane beta-barrel, and transmembrane alpha-helical. In the second step, only those fold models belonging to the determined structural class are selected for the final fold prediction. This triage method gave more predictions as well as more correct predictions compared with a simple prediction method that lacks the initial classification step. Two different schemes of assigning Bayesian model priors are presented and discussed.

Animals↗
PubMed1994

The Modified Barium Swallow Database.

Every center that carries out the modified barium swallow (MBS) has a potential storehouse of useful clinical and radiological information filed away in the patient's files and in the center's video library. The modified barium swallow database automates the recording, storage, and analysis of this information. This project utilizes a standardized clinical and radiological data form which provides a consistent approach to the reporting of the MBS results. The information on the data form is entered into the MBS database software program for decoding and permanent storage. This database program, designed for the computer novice, is menu driven to simplify operation. Once the patient information is verified on the computer screen, the program can generate different types of reports for clinical and research purposes. The program has routines to search for patients with any clinical or radiological findings of interest. The ability to group and recall patients with specific findings has been an aid in teaching, peer review, and research. The program has been modified based upon feedback and experience at three centers in Toronto that have used it for 9 months.

Barium Sulfate↗
PubMed1997

Application of molecular biology in veterinary parasitology.

The number of applications of molecular biology in veterinary parasitology is increasing rapidly. The techniques used with eukaryotic cells are generally applicable to the study of parasites and their hosts. The polymerase chain reaction is particularly important for identification and diagnosis of parasites, as well as for many other applications. With species and type specific probes or primers, sensitivities and specificities unheard of with conventional techniques can be achieved. The accumulation of more information on the DNA sequences of parasites will reveal many more unique sequences which can be used for identification, diagnosis, molecular epidemiology, vaccine development and for studying the evolutionary biology and the physiology of parasites and the host-parasite relationship. Similarly, the completion of genome projects on host organisms will greatly assist efforts to select for hosts that are genetically resistant to parasite infection. The study of the molecular biology of antiparasitic drug receptors, potential targets for chemotherapy, and the molecular genetics of drug resistance will allow molecular screens to be used with combinatorial chemistry in the search for new antiparasitic drugs, improvements to existing chemotherapeutic families and better diagnosis and monitoring of drug resistance. While there is a proliferation of molecular biology techniques, the availability of simple kits and of automated techniques and services for sequencing, library construction and oligonucleotide synthesis and other procedures is making it easier for non-specialists to apply many of the common techniques of molecular biology. Molecular biology and the benefits from its application are relevant for veterinary parasitologists in developing countries as well as developed countries and we should introduce aspects of molecular biology to the teaching and training of veterinary parasitologists.

Animals↗
PubMed2003

Ribotyping characterisation of campylobacter isolates randomly collected from different sources in Italy.

In this study the potential for using the automated PstI ribotyping as a primary library typing method to survey Campylobacter and for identification of two thermophilic Campylobacter jejuni and Campylobacter coli species was evaluated. A total of 158 isolates randomly collected in Italy from different sources were analyzed. A large percentage of chicken (28%), turkey (27%) and turkey meat (25%) isolates shared their ribotyping profiles (ribotypes) with those of humans, whereas the swine isolates had unique profiles. The identification results obtained by ribotyping corresponded to those collected by using a multiplex PCR protocol specifically designed for C. jejuni and C. coli detection. The comparison of the PstI ribotyping profiles obtained in this research with those of the isolates collected over time will facilitate determining the ribotypes that are more frequently transmitted to humans in comparison to those that are normally harboured only in animals, foods and in the environment.

Abattoirs↗
PubMed1991

PROMOT: a FORTRAN program to scan protein sequences against a library of known motifs.

Information about the three-dimensional structure or function of a newly determined protein sequence can be obtained if the protein is found to contain a characterized motif or pattern of residues. Recently a database (PROSITE) has been established that contains 337 known motifs encoded as a list of allowed residue types at specific positions along the sequence. PROMOT is a FORTRAN computer program that takes a protein sequence and examines if it contains any of the motifs in PROSITE. The program also extends the definitions of patterns beyond those used in PROSITE to provide a simple, yet flexible, method to scan either a PROSITE or a user-defined pattern against a protein sequence database.

Amino Acid Sequence↗
PubMed2005

Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates.

BACKGROUND: The laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genetic cloning and association studies. RESULTS: We show that Single Nucleotide Polymorphisms (SNPs) in commonly used rat strains are surprisingly well represented in wild rat isolates. Shotgun sequencing of 814 Kbp in one wild rat resulted in the identification of 485 SNPs as compared with the Brown Norway genome sequence. Genotyping 36 commonly used inbred rat strains showed that 84% of these alleles are also polymorphic in a representative set of laboratory rat strains. CONCLUSION: We postulate that shotgun sequencing in a wild rat sample and subsequent genotyping in multiple laboratory or domesticated strains rather than direct shotgun sequencing of multiple strains, could be the most efficient SNP discovery approach. For the rat, laboratory strains still harbor a large portion of the haplotypes present in wild isolates, suggesting a relatively recent common origin and supporting the idea that rat inbred strains, in contrast to mouse inbred strains, originate from a single species, R. norvegicus.

Animals↗
PubMed1993

Introducing health sciences librarians to the Internet.

The Internet is no longer just for the adventurous explorers or the technical experts--it has found its way into the mainstream of librarianship. New users are coming onto "the net" in droves. A wealth of information is currently available dealing with the mechanics of the Internet and there are general guides to the available resources. More work needs to be done, however, in developing subject specific materials. This paper will report on the strategy that Scott Memorial Library, Thomas Jefferson University, has employed to develop staff skills and awareness and to take advantage of the resources and opportunities that the network provides for the health sciences community.

Academic Medical Centers↗
PubMed1986

EARS: Electronic Access to Reference Service.

Electronic Access to Reference Service (EARS) is a front end to the Health Sciences Library's electronic mail system, with links to the online public catalog. EARS, which became operational in September 1984, is accessed by users at remote sites with either a terminal or microcomputer. It is menu-driven, allowing users to request: a computerized literature search, reference information, a photocopy of a journal article, or a book. This paper traces the history of EARS and discusses its use, its impact on library staff and services, and factors that influence the diffusion of new technology.

Libraries, Medical↗
PubMed1995

Dental CAD/CAM: a millstone or a milestone?

The number of dental computer-aided design/computer-aided manufacture (CAD/CAM) systems commercially available is growing. These systems range in complexity and application, from manual copy milling of inlays to full computer-controlled systems with a complex library of tooth forms enabling the automated production of crowns and bridges. All CAD/CAM systems permit the production of restorations at the chairside and, at least in theory, eliminate potential inaccuracies associated with the traditional, multistage production of indirect restorations. Their use also minimizes cross-infection. However, the capital costs of these systems are great and a high throughput of restorations is required in order to achieve financial viability. Long-term clinical studies are required before a final judgement may be made of the use of these relatively new systems.

Computer-Aided Design↗
PubMed2001

Application of an automated synthesis suite to parallel solution-phase peptide synthesis.

An in-house developed automated synthesis suite was used to prepare a library of 72 tetrapeptide derivatives, the starting materials for pharmaceutically attractive pentapeptides, employing a convergent strategy. An initial set of 18 dipeptides were synthesized on a large-scale (100-1000 g) using automated synthesis workstations, and then 72 tetrapeptides were synthesized on a medium scale (5-10 g) using an automated system. Each di- or tetrapeptide was prepared in a single operating cycle using a modified methanesulfonic acid method, then a sub-library of 56 pentapeptides were synthesized in parallel, on a small-scale (100 mg-1 g) using a robotic workstation.

Carboxylic Acids↗
PubMed2005

Fully automated synthesis of (phospho)peptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization.

BACKGROUND: Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60c-src. RESULTS: The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR) autophosphorylation site (pY1173) antibody ELISA (9H2) was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phospho)peptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of enzyme. CONCLUSIONS: The ability of this method to interface with various robotics and instrumentation is highly flexible since the microtiter plate is an industry standard. It is highly scalable by increasing the surface area within the well or the number of wells and does not require specialized robotics. The microtiter plate array system is well suited to the study of protein kinase substrates, antigens, binding molecules, and inhibitors since these all can be quantitatively studied at a single uniform, reproducible interface.

Antigen-Antibody Reactions↗
PubMed1989

Impact of DOCLINE on interlibrary loan service at the National Library of Medicine.

In March 1985, the National Library of Medicine (NLM) began implementation of DOCLINE, its automated interlibrary loan request routing and referral system. By the end of fiscal year (FY) 1987, over 1,400 biomedical libraries in all seven regions of the Regional Medical Library network were using the system. This report summarizes the findings of an analysis of the interlibrary loan (ILL) requests received in FY 1987, comparing the results with a similar analysis done in FY 1984 to describe any changes in the requests or service which might be attributable to DOCLINE implementation. DOCLINE has had a substantial impact upon ILL loan service at NLM. An increase in the number of ILL requests (35% over FY 1984) can be attributed to the speed and ease with which requests may be routed to NLM through DOCLINE. Requests which cannot be filled by local or regional libraries are automatically routed by the system to NLM as the library of last resort. NLM's fill rate for serial requests has declined, however, from 78% filled in FY 1984 to 67% filled in FY 1987. Some of the decline results from the 11,000 requests that NLM did not fill because the borrowing libraries were not willing to pay the NLM charge for filling the loans.

Humans↗
PubMed1992

Modern methods of searching the medical literature.

OBJECTIVE: To review the methods of electronic retrieval of biomedical journal articles; to demonstrate CD-ROM and online searching techniques; and to compare major biomedical databases. DESIGN: A CD-ROM MEDLINE search was made by a medical practitioner, with the assistance of an experienced librarian. An online MEDLINE/Excerpta Medica search was made by the same medical practitioner after completion of a two-day course in search techniques. The search example covered the period 1983 to 1992, and the topic was "whether steroid use for asthma/airways disease leads to osteoporosis". OUTCOMES: Search duration, article yield and search cost were assessed. RESULTS: The CD-ROM MEDLINE literature search took 60 minutes to find 31 articles (43% of the possible articles). This compared with an online search to the Bibliographic Retrieval Services database in Chicago, which produced the same articles when MEDLINE was searched (but took only 16 minutes) and which also found 47 articles (with an overlap of only seven) when Excerpta Medica was searched. We estimated that the combined MEDLINE and Excerpta Medica search detected 93% of all known relevant articles, based upon an assumed gold standard. CONCLUSIONS: Online searching is a fast and powerful alternative to CD-ROM searching. Formal training is necessary for quick and cheap reference finding. Other benefits such as direct transfer from online searching to your own computer bibliography database make online searching of biomedical databases essential to consider.

CD-ROM↗