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The human myocardial two-dimensional gel protein database: update 1994.

An updated human heart protein two-dimensional electrophoresis (2-DE) database is presented. The database, which contains some 1388 protein spots characterised in terms of M(r) and pI, has been analysed further by Western immunoblotting and protein sequencing. From a total of 103 protein spots analysed, 49 have been identified by immunoblotting and 32 have been identified by protein sequencing. A further six proteins have tentatively been assigned by comparison with the human heart 2-DE protein database of Jungblut et al. (Electrophoresis) 1994, 15, 685-607). This database is being used in studies of alterations in protein expression in the diseased and transplanted human heart.

Amino Acid Sequence

A qualitative and quantitative protein database approach identifies individual and groups of functionally related proteins that are differentially regulated in simian virus 40 (SV40) transformed human keratinocytes: an overview of the functional changes associated with the transformed phenotype.

A qualitative and quantitative two-dimensional (2-D) gel database approach has been used to identify individual and groups of proteins that are differentially regulated in simian virus 40 (SV40) transformed human keratinocytes (K14). Five hundred and sixty [35S]methionine-labeled proteins (462 isoelectric focusing, IEF; 98 nonequilibrium pH gradient electrophoresis, NEPHGE), out of the 3038 recorded in the master keratinocyte database, were excised from dry, silver-stained gels of normal proliferating primary keratinocytes and K14 cells and the radioactivity was determined by liquid scintillation counting. Two hundred and thirty five proteins were found to be either up- (177) or down-regulated (58) in the transformed cells by 50% or more, and of these, 115 corresponded to known proteins in the keratinocyte database (J.E. Celis et al., Electrophoresis 1993, 14, 1091-1198). The lowest abundance acidic protein quantitated was present in about 60,000 molecules per cell, assuming a value of 10(8) molecules per cell for total actin. The results identified individual, and groups of functionally related proteins that are differentially regulated in K14 keratinocytes and that play a role in a variety of cellular activities that include general metabolism, the cytoskeleton, DNA replication and cell proliferation, transcription and translation, protein folding, assembly, repair and turnover, membrane traffic, signal transduction, and differentiation. In addition, the results revealed several transformation sensitive proteins of unknown identity in the database as well as known proteins of yet undefined functions. Within the latter group, members of the S100 protein family--whose genes are clustered on human chromosome 1q21--were among the highest down-regulated proteins in K14 keratinocytes. Visual inspection of films exposed for different periods of time revealed only one new protein in the transformed K14 keratinocytes and this corresponded to keratin 18, a cytokeratin expressed mainly by simple epithelia. Besides providing with the first global overview of the functional changes associated with the transformed phenotype of human keratinocytes, the data strengthened previous evidence indicating that transformation results in the abnormal expression of normal genes rather than in the expression of new ones.

Autoradiography

Identification of transformation sensitive proteins recorded in human two-dimensional gel protein databases by mass spectrometric peptide mapping alone and in combination with microsequencing.

A comprehensive human keratinocyte two-dimensional (2-D) gel protein database has been established to study the expression levels and properties of the thousands of proteins that orchestrate various keratinocyte functions both in health and disease, cancer included. A major task in establishing such a database is to identify known proteins in the 2-D gel patterns as well as to reveal hitherto unknown proteins. To date, protein identification has been performed by one or a combination of the following methods: (i) comigration with known proteins, (ii) Western blotting using specific antibodies, (iii) microsequencing and (iv) vaccinia virus expression of full length cDNAs. Recently, the systematic identification of proteins has gained a new dimension with the advent of computer programs for searching peptide molecular mass databases with experimentally obtained peptide mass maps. Here we investigate this approach to identify proteins that are highly up- or down-regulated in simian virus SV40 transformed human keratinocytes (K14). Peptide mass maps of several proteins, including keratins 7, 8, 18 and 19 were obtained either by plasma desorption mass spectrometry (PDMS) analysis of high performance liquid chromatography (HPLC) purified peptides or by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of total digests. The results demonstrated that peptide mass maps can be used for a rapid and sensitive protein identification allowing fast screening of proteins recorded in 2-D gel databases. The mass spectrometric approach when combined with microsequencing strengthened identification, and added the possibility of full characterization of post-translational modifications and sequence variations.

Amino Acid Sequence

A database of protein structure families with common folding motifs.

The availability of fast and robust algorithms for protein structure comparison provides an opportunity to produce a database of three-dimensional comparisons, called families of structurally similar proteins (FSSP). The database currently contains an extended structural family for each of 154 representative (below 30% sequence identity) protein chains. Each data set contains: the search structure; all its relatives with 70-30% sequence identity, aligned structurally; and all other proteins from the representative set that contain substructures significantly similar to the search structure. Very close relatives (above 70% sequence identity) rarely have significant structural differences and are excluded. The alignments of remote relatives are the result of pairwise all-against-all structural comparisons in the set of 154 representative protein chains. The comparisons were carried out with each of three novel automatic algorithms that cover different aspects of protein structure similarity. The user of the database has the choice between strict rigid-body comparisons and comparisons that take into account interdomain motion or geometrical distortions; and, between comparisons that require strictly sequential ordering of segments and comparisons, which allow altered topology of loop connections or chain reversals. The data sets report the structurally equivalent residues in the form of a multiple alignment and as a list of matching fragments to facilitate inspection by three-dimensional graphics. If substructures are ignored, the result is a database of structure alignments of full-length proteins, including those in the twilight zone of sequence similarity.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms

Protein identification in DNA databases by peptide mass fingerprinting.

Proteins can be identified using a set of peptide fragment weights produced by a specific digestion to search a protein database in which sequences have been replaced by fragment weights calculated for various cleavage methods. We present a method using multidimensional searches that greatly increases the confidence level for identification, allowing DNA sequence databases to be examined. This method provides a link between 2-dimensional gel electrophoresis protein databases and genome sequencing projects. Moreover, the increased confidence level allows unknown proteins to be matched to expressed sequence tags, potentially eliminating the need to obtain sequence information for cloning. Database searching from a mass profile is offered as a free service by an automatic server at the ETH, Zürich. For information, send an electronic message to the address cbrg/inf.ethz.ch with the line: help mass search, or help all.

Animals

SCOP: a structural classification of proteins database for the investigation of sequences and structures.

To facilitate understanding of, and access to, the information available for protein structures, we have constructed the Structural Classification of Proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. Two search facilities are available. The homology search permits users to enter a sequence and obtain a list of any structures to which it has significant levels of sequence similarity. The key word search finds, for a word entered by the user, matches from both the text of the scop database and the headers of Brookhaven Protein Databank structure files. The database is freely accessible on World Wide Web (WWW) with an entry point to URL http: parallel scop.mrc-lmb.cam.ac.uk magnitude of scop.

Amino Acid Sequence

A sequence property approach to searching protein databases.

Currently available sequence alignment programs are generally not capable of detecting functional and structural homologs in the twilight zone of sequence similarity, i.e. when the sequence identity falls below about 25%. Here we attempt to detect such weak similarities using an approach based on a notion of protein sequence similarity radically different from that used in sequential alignment. The approach defines protein sequence dissimilarity (or distance) as a weighted sum of differences of compositional properties such as singlet and doublet amino acid composition, molecular weight, isoelectric point (protein property search or PropSearch). With PropSearch, either single sequences can be used for a database query, or multiple sequences can be merged into an "average" sequence reflecting the average composition of a protein family. First, we show that members of structural protein families have a low mutual PropSearch distance when the weights are optimized to discriminate maximally between structural families. Second, we demonstrate the results of database searches using the PropSearch method. Such searches are very rapid when scanning a preprocessed database and do not require alignments. In cases in which conventional alignment tools fail to detect similarities, PropSearch can be used to generate hypotheses about possible structural or functional relationships between a new sequence and sequences in the database.

Algorithms

DNA typing of grapevines: a universal methodology and database for describing cultivars and evaluating genetic relatedness.

With established ampelographic techniques for grapevine identification it is often difficult to achieve a satisfactory, objective result. We have developed a DNA typing system using sequence-tagged microsatellite site markers as a means of differentiating cultivars of grapevine. A semi-automated analysis procedure was linked to an electronic database and found to be an objective and reliable system for cultivar identification using this simple marker type. The accumulated DNA typing data from over eighty cultivars demonstrated that cultivars that are difficult to differentiate phenotypically using ampelographic techniques can be distinguished by DNA typing. Parentage analysis uncovered errors in parent assignment or cultivar identification in specific cases. The electronic database has a conservative format to take into account the occurrence of null alleles and the possibility of missed alleles. Computer-assisted comparisons of cultivars in the database can be performed and various approaches for estimating the match probability that two unrelated cultivars have the same genotype simply due to chance are discussed. We suggest that further development of the database through international co-operation using standardised sequence-tagged site markers offers the possibility of achieving a universal grapevine identification system.

DNA, Plant

Database for serial magnetic resonance imaging in multiple sclerosis.

The unique sensitivity of magnetic resonance imaging (MRI) in detecting disease activity in multiple sclerosis (MS) and the objective nature of the information obtained suggest that MRI will be a useful and reliable way of monitoring treatment trials. There is a need to develop an appropriate database which would provide a standardised means of assessment, not only of MRI, but also of essential clinical information. As part of the program of Concerted Action in Multiple Sclerosis, funded by the Commission of the European Community (CEC), we have developed a database for recording serial brain MRI results. The database consists of core, entry and follow-up sections. Both entry and follow-up parts are subdivided into clinical, MR system and MRI data. We expect that the use of this database will maximise efficiency of MRI monitoring in MS treatment trials, particularly in multicentre studies.

Brain

A relational database for sequence-specific protein NMR data.

A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and atom-specific assignments, and experimental conditions. At present, all data are entered from the primary refereed literature. Examples are given of sample queries to the database. Possible distribution formats are discussed.

Animals

A database of lipid phase transition temperatures and enthalpy changes.

The systematic study of the mesomorphic phase properties of synthetic and biologically derived lipids began some 30 years ago. In the past decade, interest in this area has grown enormously. As a result, there exists a wealth of information on lipid phase behavior, but unfortunately these data have, until now, been scattered throughout the literature in a variety of books, proceedings and journals. The data have recently been compiled in a centralized database with a view to providing ready access to same and to the appropriate literature. The compilation facilitates review of what has thus far been accomplished and highlights what remains to be done in this active research area. As such, it represents a convenient summary of the existing data which, when evaluated, will enable us to identify where deficits exist in the data, to reveal the fundamental physicochemical principles upon which lipid phase behavior is based and to understand more completely lipid phase relations in biological, reconstituted and formulated systems. The compilation consists of a tabulation of all known mesomorphic and polymorphic phase transition temperatures and enthalpy changes for synthetic and biologically-derived lipids in the dry and in the partially and fully hydrated states. Also included is the effect on these thermodynamic values of pH, and of salt and metal ion concentration and other additives such as proteins, drugs, etc. The methods used in making the measurements and the experimental conditions are reported. Bibliographic information includes complete literature referencing and list of authors. As of this writing, the database is current through June, 1990 and contains in excess of 9500 records. Each record contains 28 fields. Here, we describe how the database originated, its scope and contents, data abstraction procedures, and issues relating to mesophase and lipid nomenclature, data analysis and evaluation, and database maintenance and distribution.

Databases, Factual

Integrating knowledge-based systems and databases.

In recent years, there has been an explosion of interest among the computing community in the field of artificial intelligence, particularly in the areas of natural language processing and knowledge-based systems (KBS). The medical domain has seen the development of hundreds of KBSs and there is substantial evidence to show that the application of a knowledge-based approach to decision support can go a long way towards overcoming the information overload experienced by many clinicians today. Yet many of these medical KBSs are still at the prototype stage and are mainly confined to research laboratories. There are many reasons for this apparently slow take-up of the technology, but one of the most significant is the lack of integration into the regular routine information processing of the organisation, in particular the database processing. This paper discusses the benefits of such integration and methods for achieving it in the context of general trends in information systems. Database technology provides efficient and secure management of large amounts of data in a multi-user, multi-application environment. Knowledge-based technology, on the other hand, provides mechanisms for building intelligent systems. Thus, for example, given a set of facts about a domain (symptoms, laboratory test results, etc.) together with a set of rules which apply to that domain (e.g. 'if TT4 > 150 nmol/l then suspect hyperthyroidism'), a KBS can deduce new information about that domain automatically. The effective integration of these two technologies is seen as a means of achieving the intelligent information systems of the future. There are three basic approaches to integrating KBSs and databases. The first is to start with the KBS and incorporate data management functions. Alternatively, intelligence from the KBS can be incorporated into the database. Finally, the two systems can be allowed to co-exist as independent systems which can talk to each other by means of standard interfaces. There are many advantages to this last approach since it offers much more flexibility and extensibility and is consistent with the general trend in computing towards open systems.

Artificial Intelligence

Extended relational operators for statistical data manipulations in medical databases.

Conventional relational database management systems fail to address three features of statistical data management in a biomedical/clinical database, namely, that (1) statistical and medical data (SMD) require a great deal of space and need to be stored in a reduced form with minimal duplication; indeed, SMD have many derived/calculated and summary statistics that make the number of attributes in a relation (i.e., a set of records) grow rapidly and dynamically; (2) most SMD have hierarchical structures that are difficult to manage using the relational data model since SMD are stored in separate relations for duplication and space considerations; and (3) the management of SMD is made easier if it is possible to reorganize relations or group data, a capability lacking in conventional relational database management systems. In this paper, we (1) introduce five extended relational operators, (lattice) NEST, (lattice) UNNEST, MERGE, SPREAD, and GEN, to reorganize relations; (2) integrate the extended operators with conventional relational algebra and introduce the concept of the lattice relational model; and (3) give applications of the extended relational operators and the lattice relational model in solving the problems of statistical data manipulation in medical databases.

Database Management Systems

Establishing a consultation-liaison psychiatry clinical database in an Australian general hospital.

This paper describes the institution of a clinical database in the consultation-liaison psychiatry service of an Australian general hospital psychiatry unit. One of the problems faced was that many researchers and clinicians in Australia use the ICD-9 rather than the DSM-III-R classification system. Nevertheless, it was possible to use the DSM-III-R-based MICRO-CARES clinical database management system in this project. The data obtained during the first 12 months of its use are presented. Despite differences in the patient demographic characteristics, the data obtained are within the ranges described for North American and European sites. The local benefits of such a clinical database are described, and it is argued that such a database is also necessary for interhospital and international collaborative studies and comparisons.

Adult

The PDQ (Physician Data Query), the cancer database, in oncological clinical practice.

The above illustrates the fact that a physician interested in consulting the PDQ database must dedicate a certain amount of time to an analytical review of the database. It is difficult to determine how much time is required to acquire a sufficient level of control because there are many variables affecting the learning time: experience in using computerized systems, cultural background, personal inclination, etc. However, a certain amount of caution and humility should be exercised whenever a physician approaches a database of this type for the first time, in order to avoid the mistake of dangerously underestimating the nature of the problem. On the other hand, the physician's specific competence and professionalism will not be questioned at all, since they are fundamental to obtain productive search results. If, indeed, the above discussion focussed heavily on the most closely documental aspect of the problem, it should not be forgotten that the contents of the database can be fully understood only by experts who are used to encountering certain terms and procedures on a daily basis. In fact, when a physician turns to a documentation center for a PDQ research, the physician's assistance is always requested in order pair clinical and documental competence. It is this second skill that the physician must acquire to become totally independent.

Databases, Factual

ATSDR's information databases to support human health risk assessment of hazardous substances. Agency for Toxic Substances and Disease Registry.

The American public, like persons in many other nations, is concerned about the potential adverse impacts of uncontrolled hazardous wastes. The concerns are often predicated on the fear that adverse health effects will occur because of releases of hazardous substances into community environments. To respond to these concerns, government agencies and private sector organizations must rely on credible, accessible, up-to-date information databases. These databases should be relevant to the needs of the people who respond to uncontrolled releases of hazardous substances. Of particular importance are databases that profile the toxicity of hazardous substances and other information useful to physicians and other health care providers. This paper describes how the federal Agency for Toxic Substances and Diseases Registry (ATSDR) has developed several toxicologic and human health information databases under mandates in the Superfund statute for responding to the public's concerns about hazardous substances.

Databases, Factual

Review of Papyrus bibliographic database software.

Papyrus is an inexpensive bibliographic database which provides some features not found in other similar packages. Its flexibility in handling references of many types and formats, its capacity for integration with manuscripts prepared with word processors, its capacity for importing references from national databases and its ability to perform microcosmic literature searches are attractive features. Because Papyrus has tackled a complex task, mastery of the intricacies of the program may present a substantial challenge to novice computer users. Although the manipulation of an existing customized bibliographic database would seem to be attractive for any researcher or author who prepares manuscripts for publication, the optimal use of the program also requires an extensive commitment of time and labor for the initial entry of all pertinent references into the database. While this could be accomplished gradually in conjunction with the preparation of individual manuscripts, the creation of a complete file of references could require hundreds of hours of labor. Individual authors, as well as larger research groups, should be prepared for this type of commitment before acquiring the Papyrus system.

Bibliographies as Topic

An adjuvant database for preclinical evaluation of vaccines and immunotherapeutics.

Adjuvants are immunostimulators used to enhance vaccine efficacy against infectious diseases. However, current methods for evaluating their efficacy and safety are limited, hindering large-scale screening. To address this, we developed a prototype Adjuvant Database (ADB) containing transcriptome data, generated using the same protocols as the widely used Open TG-GATEs (OTG) toxicogenomics database, covering 25 adjuvants across multiple species, organs, time points, and doses. This enabled cross-database integration of ADB and OTG. Transcriptomic patterns successfully distinguished each adjuvant regardless of organs or species. Using both databases, we built machine learning models to predict adjuvanticity and hepatotoxicity. Notably, we identified colchicine's adjuvant activity and FK565's liver toxicity through data-driven analysis. Overall, ADB combined with OTG offers a framework for transcriptomics-based, data-driven screening of adjuvant candidates.

Animals