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PubMed1981

Rapid cataloging of ribonuclease T1 resistant oligonucleotides from ribosomal RNAs for phylogenetic studies.

A rapid and simple method of oligonucleotide cataloging for phylogenetic studies is presented. It involves in vitro 5'-32P-labelling of RNase T1 - resistant oligonucleotides of ribosomal 16S RNA and finger-printing by high voltage electrophoresis and gradient thinlayer chromatography. Oligonucleotide sequences are established by the mobility shift method, using controlled alkali cleavage, high voltage electrophoresis and homochromatography. These procedures facilitate in particular the analysis of long RNase T1 - resistant oligonucleotides. Oligonucleotide catalogs are established fo three Actinomycetes, namely Oerskovia turbata, Actinoplanes philippinensis and Ampullariella regularis. These catalogs are equivalent to those obtained by methods which were described by Sanger and Woese.

Actinomyces↗
PubMed1984

16S rRNA oligonucleotide catalog data base.

We have developed a package of programs to create, maintain and manipulate a data base of 16S rRNA oligonucleotide catalog data. For the first time all the published catalog data is brought together in one place in a readily usable form. The package allows generation of dendrograms, facilitates searches for related oligonucleotides between catalogs, and allows construction of global and local dictionaries. Interactive capabilities allow for searches of the dictionary as well as an associated file of likely oligonucleotide families.

Base Sequence↗
PubMed2000

An annotated catalog of inverted repeats of Caenorhabditis elegans chromosomes III and X, with observations concerning odd/even biases and conserved motifs.

We have taken a computational approach to the problem of discovering and deciphering the grammar and syntax of gene regulation in eukaryotes. A logical first step is to produce an annotated catalog of all regulatory sites in a given genome. Likely candidates for such sites are direct and indirect repeats, including three subcategories of indirect repeats: inverted (palindromic), everted, and mirror-image repeats. To that end we have produced a searchable database of inverted repeats of chromosomes III and X of Caenorhabditis elegans, the first completely sequenced multicellular eukaryote. Initial results from the use of this catalog are observations concerning odd/even biases in perfect IRs. The potential usefulness of the catalog as a discovery tool for promoters was shown for some of the genes involved with G-protein functions and for heat shock protein 104 (hsp104).

Algorithms↗
PubMed2006

Microbial identification by mass cataloging.

BACKGROUND: The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample.Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms. RESULTS: Ribonuclease T1 and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T1 of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individual fragments or combinations thereof can be used to recognize the presence of specific organisms in a complex sample. In this regard, 140 strains out of 1,921 organisms (7.3%) could be identified by the presence of a unique RNase T1-generated oligoribonucleotide mass. Combinations of just two and three oligoribonucleotide masses allowed 54% and 72% of the specific strains to be identified, respectively. An initial algorithm for recovering likely organisms present in complex samples is also described. CONCLUSION: The use of catalogs of compositions (masses) of characteristic oligoribonucleotides for microbial identification appears extremely promising. RNase T1 is more useful than ribonuclease A in generating characteristic masses, though RNase A produces oligomers which are more readily distinguished due to the large mass difference between A and G. Identification of multiple species in mixtures is also feasible. Practical applicability of the method depends on high performance mass spectrometric determination, and/or use of methods that increase the one dalton (Da) mass difference between uracil and cytosine.

Algorithms↗
PubMed2005

A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs.

BACKGROUND: In recent years, intensive computational efforts have been directed towards the discovery of promoter motifs that correlate with mRNA expression profiles. Nevertheless, it is still not always possible to predict steady-state mRNA expression levels based on promoter signals alone, suggesting that other factors may be involved. Other genic regions, in particular 3' UTRs, which are known to exert regulatory effects especially through controlling RNA stability and localization, were less comprehensively investigated, and deciphering regulatory motifs within them is thus crucial. RESULTS: By analyzing 3' UTR sequences and mRNA decay profiles of Saccharomyces cerevisiae genes, we derived a catalog of 53 sequence motifs that may be implicated in stabilization or destabilization of mRNAs. Some of the motifs correspond to known RNA-binding protein sites, and one of them may act in destabilization of ribosome biogenesis genes during stress response. In addition, we present for the first time a catalog of 23 motifs associated with subcellular localization. A significant proportion of the 3' UTR motifs is highly conserved in orthologous yeast genes, and some of the motifs are strikingly similar to recently published mammalian 3' UTR motifs. We classified all genes into those regulated only at transcription initiation level, only at degradation level, and those regulated by a combination of both. Interestingly, different biological functionalities and expression patterns correspond to such classification. CONCLUSION: The present motif catalogs are a first step towards the understanding of the regulation of mRNA degradation and subcellular localization, two important processes which--together with transcription regulation--determine the cell transcriptome.

3' Untranslated Regions↗
PubMed1965

MECHANIZATION OF LIBRARY PROCEDURES IN THE MEDIUMSIZED MEDICAL LIBRARY: 3. ACQUISITIONS AND CATALOGING.

A system is described for producing acquisitions and fiscal records, new book lists, and book catalogs of nonserial works from a single punched card input, manipulated by a computer under the control of programs written for the task. All parts of the system are now in operation except the production of the subject portion of the book catalog, for which the program is now (March 1965) being developed and which is expected to be in operation by summer.

Books↗
PubMed1992

Completeness of catalogs of autosomal dominant, autosomal recessive, and X-linked phenotypes.

The completeness of McKusick's catalogs of Mendelian Inheritance in Man (MIM) as to the number of phenotypes included was studied by estimating the degree of concordance with the Dutch Gene Catalog of the Department of Medical Genetics of the University of Groningen, The Netherlands. On a total of 355 Mendelian phenotypes described in persons living in The Netherlands or originating from this country, there were nine disease entities which were not present in MIM. As judged from this comparison MIM attains 97.5% completeness (95% CI: 95.3-98.7%). Similar comparisons with data from other countries are needed before a final conclusion can be reached. Corresponding contributors in different countries or linguistic areas might further improve MIM's completeness.

Catalogs as Topic↗
PubMed1999

Maintaining a catalog of manually-indexed, clinically-oriented World Wide Web content.

With no quality controls and a highly distributed means of posting information, finding high-quality, clinically-oriented content on the World Wide Web can be difficult. Maintaining a catalog of such information can be equally challenging. CliniWeb is a catalog of quality-filtered and clinically-oriented content on the Web designed to enhance access to such information. This paper describes a group of semi-automated tools have been developed to maintain the CliniWeb database. One allows easier identification of content by utilizing Web crawling techniques from high-level pages. Another allows easier selection of content for inclusion and its indexing. A final one checks links to help keep the database current. These are augmented by general plans to adopt more detailed metadata and linkages into the medical literature.

Abstracting and Indexing↗
PubMed1987

Beyond the online catalog: developing an academic information system in the sciences.

The online public access catalog consists essentially of a machine-readable database with network capabilities. Like other computer-based information systems, it may be continuously enhanced by the addition of new capabilities and databases. It may also become a gateway to other information networks. This paper reports the evolution of the Bibliographic Access and Control System (BACS) of Washington University in end-user searching, current awareness services, information management, and administrative functions. Ongoing research and development and the future of the online catalog are also discussed.

Catalogs, Library↗
PubMed1969

Regional utilization of the union catalog of medical periodicals system.

This paper describes regional utilization of the Union Catalog of Medical Periodicals system and data base in producing union lists outside Metropolitan New York, the area served by the Union Catalog. A basic introduction to the Medical Library Center of New York's UCMP system is set forth, demonstrating the system's value in the production of such medical and paramedical union lists throughout the country. Several applications are then described, showing how these union lists were produced.

Catalogs, Union as Topic↗
PubMed1977

Audiovisual materials: a survey of bibliographic controls in distributors' catalogs.

The current pattern of bibliographic control in audio-visual distributors' catalogs is described. Eight bibliographic control elements are defined, and the criteria for evaluating the occurrence of these elements in sixty-four sample catalogs are specified. When the distributors are grouped according to category, such as educational or commercial, the pattern of bibliographic control has three distinct clusters of elements. When the distributors are grouped by the number of titles handled, there is no clear pattern. The implications of these patterns are discussed in terms of practical library reference services. A solution to the problem of bibliographic control of health science audiovisual materials is proposed.

Audiovisual Aids↗
PubMed1983

The NEOUCOM Cooperative Cataloging Service: development and review of the first four years.

The Basic Medical Sciences Library of the Northeastern Ohio Universities College of Medicine (NEOUCOM) provided a Cooperative Cataloging Service to fourteen of its affiliated hospitals' libraries since March 1978, using the OCLC system. Analysis of the first four years of service showed that the hospital libraries spent almost $30,000 to catalog more than 18,000 titles. Personnel expenses and other costs eclipsed the savings from a 31.3% duplication rate. Centralized bibliographic control control and the principal by-product of the service, a uniform, machine-related data base, provided the foundation for an on-line integrated library system to serve the consortium. The hospital libraries contributed 44% of the unique titles in this data base, which emphasis the need to share resources and continue cooperation.

Cataloging↗
PubMed1980

Descriptive cataloging of serials: the National Library of Medicine versus the Library of Congress.

Descriptive cataloging practices for serial differ significantly in some respects between the Library of Congress and the National Library of Medicine. This paper compares some of these differences and indicates the impact they can have on the development of on-line cooperative data bases such as OCLC. Attention is also given to the possible impact of the second edition of the Anglo-American Cataloguing Rules on serials cataloging. The need for standardization is stressed.

Cataloging↗
PubMed2026

A genomic catalog of Earth's bacterial and archaeal symbionts.

Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth yet remains underexplored because of culturing challenges. This study used machine learning (ML) to predict symbiotic lifestyles in more than a hundred thousand microbial genomes from diverse environmental metagenome samples and reference genomes. Predictions were performed using symclatron, an ML framework developed to identify genomic signatures of symbionts. Predictions were deposited in a catalog we established called Symbiont Genomes (SymGs). The results indicate that 15-23% of uncultivated microorganisms likely engage in symbiotic relationships with other organisms, categorized as host-associated or obligate intracellular lifestyles, and are present in half of all known bacterial and archaeal phyla. We also identify genomic signatures of symbiotic lifestyles, including the loss of certain metabolic functions and the differential presence of metabolic modules that may enable host-dependent living. The symclatron software and the SymGs catalog represent valuable resources for studying symbioses, potentially facilitating future mechanistic investigations and engineering of host-microorganism associations.

Journal Article↗
PubMed1969

Homogeneous catalogs of earthquakes.

The usual bias in earthquake catalogs against shocks of small magnitudes can be removed by testing the randomness of the magnitudes of successive shocks. The southern California catalog, 1933-1967, is found to be unbiased in the sense of the test at magnitude 4 or above; the cutoff is improved to M = 3 for the subcatalog 1953-1967.

Journal Article↗
PubMed1999

The catalog of human hair keratins. I. Expression of the nine type I members in the hair follicle.

The human type I hair keratin subfamily comprises nine individual members, which can be subdivided into three groups. Group A (hHa1, hHa3-I, hHa3-II, hHa4) and B (hHa7, hHa8) each contains structurally related hair keratins, whereas group C members hHa2, hHa5, and hHa6 represent structurally rather unrelated hair keratins. Antibodies produced against these individual hair keratins, first analyzed for specificity by one- dimensional Western blots of total hair keratins, were used to establish the two-dimensional catalog of the human type I hair keratin subfamily. The catalog comprises two different series of type I hair keratins: a strongly expressed, Coomassie-stainable series containing hair keratins hHa1, hHa3-I/II, hHa4, and hHa5, and a weakly expressed, immunodetectable series harboring hHa2, hHa6 hHa7, and hHa8. In situ hybridization and immunohistochemical expression studies on scalp follicles show that two hair keratins, hHa2 and hHa5, define the early stage of hair differentiation, i.e. hHa5 expression in hair matrix and hHa5/hHa2 coexpression in the early hair cuticle cells. Whereas cuticular differentiation proceeds without the expression of further type I hair keratins, matrix cells embark on the cortical pathway by sequentially expressing hHa1, hHa3-I/II, and hHa4, which are supplemented by hHa6 at an advanced stage of cortical differentiation, and hHa8, which is expressed heterogeneously in cortex cells. Thus, six type I hair keratins are involved in the terminal differentiation of anagen hairs. The expression of hHa7 is conspicuously different from that of the other hair keratins in that it does not occur in the large anagen follicles of terminal scalp hairs but only in central cortex cells of the rare and small follicle type that gives rise to vellus hairs.

Blotting, Western↗
PubMed2005

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

We describe a comprehensive map of putative transcription factor binding sites (TFBSs) across multiple genomes created using a search method that relies on hidden Markov models built from experimentally determined TFBSs. Using the information in the TRANSFAC and JASPAR databases, we built 1134 models for TFBSs and used them to scan regions 10 kb upstream of the start of the transcript for all known genes in the human, mouse and Drosophila melanogaster genomes. The results, together with homology information on clusters of ortholog genes across the three genomes, were used to create a multi-organism catalog of annotated TFBSs. The catalog can be queried through a web interface accessible at http://bio.chip.org/mapper that allows the identification, visualization and selection of TFBSs occurring in the promoter of a gene of interest and also the common factors predicted to bind across the cluster of orthologs that includes that gene. Alternatively, the interface allows the user to retrieve binding sites for a single transcription factor of interest in a single gene or in all genes of the human, mouse or fruit fly genomes.

Animals↗