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R D Appel

Publications and source records attributed to R D Appel.

At least 55 records · Page 3Linked to original sources
PubMed1996

From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis.

Separation and identification of proteins by two-dimensional (2-D) electrophoresis can be used for protein-based gene expression analysis. In this report single protein spots, from polyvinylidene difluoride blots of micropreparative E. coli 2-D gels, were rapidly and economically identified by matching their amino acid composition, estimated pI and molecular weight against all E. coli entries in the SWISS-PROT database. Thirty proteins from an E. coli 2-D map were analyzed and identities assigned. Three of the proteins were unknown. By protein sequencing analysis, 20 of the 27 proteins were correctly identified. Importantly, correct identifications showed unambiguous "correct" score patterns. While incorrect protein identifications also showed distinctive score patterns, indicating that protein must be identified by other means. These techniques allow large-scale screening of the protein complement of simple organisms, or tissues in normal and disease states. The computer program described here is accessible via the World Wide Web at URL address (http:@expasy.hcuge.ch/).

Amino Acids↗
PubMed1995

Inside SWISS-2DPAGE database.

Several two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) databases have been established and updated for more than 15 years. Only recently have developments of computer networks and high-speed transfer protocols provided the required tools for sharing comprehensive and hypermedia 2-D PAGE databases. This publication describes the SWISS-2DPAGE database structure. Proteins present in samples of human tissue, cells, cell lines and body fluids are assembled and described in an accessible uniform format. SWISS-2DPAGE can be freely accessed through the World-Wide Web (WWW) network on the ExPASy molecular biology server.

Body Fluids↗
PubMed1995

Differential protein expression in aortic smooth muscle cells cultured from newborn and aged rats.

Atherosclerosis is a complex disease in which smooth muscle cells (SMC) play a fundamental role. Work from several laboratories has suggested that in experimental models of atheromatosis SMC heterogeneity is important in the establishment of intimal thickening. Moreover it has been shown that SMC cultured from different situations in vivo maintain distinct phenotypic features in vitro. In order to find proteins differentially expressed in SMC cultured from newborn and aged rats, total protein extracts were separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), high-resolution maps were built, and differentially expressed spots were identified by automatic computer analysis. Of the 14 differentially expressed protein spots, 4 were present in SMC of newborn and 10 in SMC of old animals; we describe their molecular weights and isoelectric points. One of these proteins (expressed only in cultured SMC of old rats) was successfully microsequenced for 16 amino acids and it was found identical to cellular retinol-binding protein. This results provides, to our knowledge, the first suggestion that retinoids are implicated in the differentiation and aging of vascular SMC.

Aging↗
PubMed1995

Sharing of worldwide spread knowledge using hypermedia facilities & fast communication protocols (Mosaic and World Wide Web): the example of ExPASy.

The sharing of knowledge worldwide using hypermedia facilities and fast communication protocols (i.e., Mosaic and World Wide Web) provides a growth capacity with tremendous versatility and efficacy. The example of ExPASy, a molecular biology server developed at the University Hospital of Geneva, is striking. ExPASy provides hypermedia facilities to browse through several up-to-date biological and medical databases around the world and to link information from protein maps to genome information and diseases. Its extensive access is open through World Wide Web. Its concept could be extended to patient data including texts, laboratory data, relevant literature findings, sounds, images and movies. A new hypermedia culture is spreading very rapidly where the international fast transmission of documents is the central element. It is part of the emerging new "information society".

Artificial Intelligence↗
PubMed1994

The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis.

SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), created and maintained at the University Hospital of Geneva in collaboration with the Department of Medical Biochemistry of Geneva University. The proteins have been identified on various 2-D PAGE reference maps by microsequencing, immunoblotting, gel comparison and amino acid composition.

Blotting, Western↗
PubMed1993

Human liver protein map: update 1993.

This publication updates the reference human liver protein map. By microsequencing, 27 spots or 34 polypeptide chains were identified. The most abundant polypeptides detected on the silver stained liver map were key elements in major hepatic biochemical pathways. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing the 1993 reference human liver SWISS-2DPAGE database. SWISS-2DPAGE and the SWISS-PROT protein sequence databases are closely linked together through the use of common accession numbers.

Amino Acid Sequence↗
PubMed1993

Plasma and red blood cell protein maps: update 1993.

This publication updates the reference plasma and red blood cell protein maps obtained with immobilized pH gradients. Seventeen polypeptide spots or chains were partially characterized by direct N-terminal sequencing or by sequencing of peptides obtained from enzymatic digestion. Additional new polypeptides and previously known proteins are listed in a table and/or labeled on the protein maps, thus providing the 1993 update of the human plasma and red blood cell two-dimensional gel SWISS-2DPAGE database. SWISS-2DPAGE and the SWISS-PROT protein sequence databases are closely linked together through the use of common accession numbers.

Amino Acid Sequence↗
PubMed1993

SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images.

This publication presents the SWISS-2DPAGE database which gathers data on proteins identified on various two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) maps. Each SWISS-2DPAGE entry contains data on one protein, including mapping procedures, physiological and pathological data and bibliographical references, as well as several 2-D PAGE images showing the protein location. Links are also provided to other databases such as SWISS-PROT, EMBL, PROSITE and OMIM. The database has been set up on a server which may be accessed from any computer connected to the internet and it also makes it possible to display the theoretical location of proteins, the positions of which are not yet known on the 2-D PAGE.

Databases, Factual↗
PubMed1991

The MELANIE project: from a biopsy to automatic protein map interpretation by computer.

The goals of the MELANIE project are to determine if disease-associated patterns can be detected in high resolution two-dimensional polyacrylamide gel electrophoresis (HR 2D-PAGE) images and if a diagnosis can be established automatically by computer. The ELSIE/MELANIE system is a set of computer programs which automatically detect, quantify, and compare protein spots shown on HR 2D-PAGE images. Classification programs help the physician to find disease-associated patterns from a given set of two-dimensional gel electrophoresis images and to form diagnostic rules. Prototype expert systems that use these rules to establish a diagnosis from new HR 2D-PAGE images have been developed. They successfully diagnosed cirrhosis of the liver and were able to distinguish a variety of cancer types from biopsies known to be cancerous.

Biopsy↗
PubMed1991

Multiple elevations of cytosolic-free Ca2+ in human neutrophils: initiation by adherence receptors of the integrin family.

Multiple spontaneous transient elevations of cytosolic-free calcium ([Ca2+]i) are observed in single human neutrophils during adherence. The interrelation between adherence and spontaneous [Ca2+]i transients was analyzed by simultaneous monitoring of [Ca2+]i and cell morphology. Fluorescent images of fura 2-loaded neutrophils attached to albumin-coated glass were recorded with a high sensitivity CCD camera while [Ca2+]i was assessed with a dual excitation microfluorimetry. The majority of the initially round cells studied showed changes in shape which started either before or at the same time as the onset of the [Ca2+]i transients. These data suggested that a rise in [Ca2+]i is not a prerequisite for shape change. This conclusion was confirmed by observation of movement and spreading in cells whose [Ca2+]i transients were abolished by chelation of extracellular Ca2+. Instead, our data suggest that spreading or adhesion itself initiates the [Ca2+]i activity. In keeping with this hypothesis, cytochalasin B, which prevents both cell movement and adhesion, completely inhibited generation of [Ca2+]i transients. To determine if the movement alone or adhesion alone is responsible for [Ca2+]i activity, we treated cells with antibodies against the beta chain (CD18, beta 2) or the alpha subunit (CD11b, alpha m) of the dominant leukocyte integrin (CR3). Antibody-treated cells showed normal extension of pseudopods but impaired ability to adhere. Inhibition of adhesion in this way inhibited [Ca2+]i activity. Taken together these results suggest that following sequence of events after contact of neutrophils with surfaces: (a) cell movement and shape change lead to enhanced contact of integrins with the surface; and (b) integrins-mediated adhesion generates multiple [Ca2+]i transients. The [Ca2+]i transients may then control exocytic events associated with movement and may provide a link between adherence and activation or priming of neutrophils to other stimuli.

Antibodies, Monoclonal↗
PubMed1990

From biopsy to automatic diagnosis.

High resolution two-dimensional gel electrophoresis is a very powerful biochemical tool for analysis of complex protein mixtures. In well defined situations, protein maps, obtained from tissue biopsies or biological fluids by this technique, can be automatically analyzed by computer. Some polypeptide patterns are the fingerprints of diseases. Applying clustering algorithm and learning techniques, the prototype expert system MELANIE recognized patterns and associated the correct diagnosis to the specific pattern.

Diagnosis, Computer-Assisted↗
PubMed1988

Computerized classification of two-dimensional gel electrophoretograms by correspondence analysis and ascendant hierarchical clustering.

A powerful data processing methodology for analysis and classification of two-dimensional gels is introduced. The approach is based on correspondence analysis (CA) and ascendant hierarchical classification (AHC), and significantly differs from the more classical principal-component decomposition. Starting with a series of gels, each having a large number of spots, CA allows their representation in a factorial space of reduced dimension; classification into meaningful groups is then performed using AHC. Simultaneous representation of both spots and gels in the same space can be done. This precisely indicates the key spots pertinent for the classification, and therefore the characteristic proteins representative of a particular class of gels (i.e. of a particular disease or biological status). In addition, knowledge of these characteristic spots greatly simplifies the screening of future gels. After a brief overview of the Mélanie system for analyzing 2D gels, the theory of correspondence analysis and ascendant hierarchical classification is summarized. Equations are given that are easily ammenable to computation. How classification of two-dimensional gel electrophoretograms is accomplished is then detailed. Experimental results support the power of this approach.

Cluster Analysis↗
PubMedDate not supplied

Detailed peptide characterization using PEPTIDEMASS--a World-Wide-Web-accessible tool.

In peptide mass fingerprinting, there are frequently peptides whose masses cannot be explained. These are usually attributed to either a missed cleavage site during the chemical or enzymatic cutting process, the lack of reduction and alkylation of a protein, protein modifications like the oxidation of methionine, or the presence of protein post-translational modifications. However, they could equally be due to database errors, unusual splicing events, variants of a protein in a population, or artifactual protein modifications. Unfortunately the verification of each of these possibilities can be tedious and time-consuming. To better utilize annotated protein databases for the understanding of peptide mass fingerprinting data, we have written the program "PEPTIDEMASS". This program generates the theoretical peptide masses of any protein in the SWISS-PROT database, or of any sequence specified by the user. If the sequence is derived from the SWISS-PROT database, the program takes into account any annotations for that protein in order to generate the peptide masses. In this manner, the user can obtain the predicted masses of peptides from proteins which are known to have signal sequences, propeptides, transit peptides, simple post-translational modifications, and disulfide bonds. Users are also warned if any peptide masses are subject to change from protein isoforms, database conflicts, or an mRNA splicing variation. The program is freely accessible to the scientific community via the ExPASy World Wide Web server, at the URL address: http://www.expasy.ch/www/tools.html.

Amino Acid Sequence↗
PubMedDate not supplied

Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: the example of Escherichia coli.

Knowledge-based molecular modelling of proteins has proven useful in many instances, including the rational design of mutagenesis experiments, but it has generally been limited by the availability of expensive computer hardware and software. To overcome these limitations, we developed the SWISS-MODEL server for automated knowledge-based protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein models for sequences which share significant similarities with at least one protein of known three-dimensional structure. We have now used the software framework of the server to generate large collections of protein models, and established the SWISS-MODEL Repository, a new database for automatically generated and theoretical protein models. This repository is directly integrated with the SWISS-PROT and SWISS-2DPAGE databases through the ExPASy World Wide Web server (URL is http://expasy.hcuge.ch). Here we present an illustration of this process by an application to the Escherichia coli sequences.

Bacterial Proteins↗
PubMedDate not supplied

Simultaneous analysis of cyclin and oncogene expression using multiple monoclonal antibody immunoblots.

Cell dysfunction or dysregulation in cancer generally results from complex gene interactions, numerous cellular events and environmental influences which modify gene expression or post-translational protein modifications. Genetic analysis in itself cannot always predict or diagnose multigenic diseases. The major technical difficulty is thus to detect, identify and measure simultaneously the expression of several genes and the post-translational modifications of their products. In order to progress to this direction, this paper describes a simple immunoblot method using several monoclonal anti-bodies to simultaneously analyze oncogene expression and cell cycle specific checkpoints in patient solid biopsies and transformed cell lines. One mg of normal human liver biopsy and HEPG2 (hepatoblastoma-derived cell line) protein samples have been separated by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and transferred onto polyvinylidene difluoride (PVDF) membranes. The membranes were stained with amido black, scanned and tested separately with the nine monoclonal antibodies p53, c-myc, PCNA, MEK1, pan-ras, Cip1, Cdc2, Kip1, and TCTP. The nine antibodies of interest were then combined to form a mixture, and simultaneously used as the primary antibodies. This antibody mixture simultaneously detected the nine proteins of interest on both samples and it demonstrated the extensive expression changes and the presence of various isoforms most likely due to post-translational modifications of gene products.

Antibodies, Monoclonal↗
PubMedDate not supplied

MARVIN, multi-agent softbot to retrieve multilingual medical information on the Web.

The World-Wide Web is an unstructured, multimedia and multilingual information network. While most efforts have addressed the structuring issue, very few attempts have been proposed to provide support for multilingual information retrieval. Yet, medical information is now available all over the world. The MARVIN (Multi-Agent Retrieval Vagabond on Information Network) softbot and its associated medical search engine MedHunt (Medical Hunter) are a solution for helping people, who only understand a few languages, to access multilingual information.

Information Storage and Retrieval↗