PubMed Health⌕ Search

Biomedical subjects

J Snoddy

Publications and source records attributed to J Snoddy.

8 recordsLinked to original sources
PubMed2005

GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

BACKGROUND: The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. RESULTS: GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments. CONCLUSION: GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets.

Algorithms↗
PubMed1993

Structure-activity relationships of trans-3,4-dimethyl-4-(3-hydroxyphenyl)piperidine antagonists for mu- and kappa-opioid receptors.

A series of racemic N-substituted trans-3,4-dimethyl-4-(3-hydroxyphenyl)piperidines were evaluated for opioid agonist and antagonist activity at mu and kappa receptors. Several highly potent mu and kappa antagonists were discovered; however, no compounds with high selectivity for either the mu or kappa receptor were identified. Importantly, no derivative was found to have significant opioid agonist activity. Two derivatives were resolved, and the activities of the enantiomers were investigated. Only a limited stereochemical effect on opioid receptor selectivities was observed. The structure-activity relationships described establish the existence of an important lipophilic binding site distal to the nitrogen for both mu and kappa receptors and confirm the pure opioid antagonist pharmacophore nature of the trans-3,4-dimethyl-4-(3-hydroxyphenyl)piperidine structure.

Analgesia↗
PubMed1993

DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing.

The concept of sequencing by hybridization (SBH) makes use of an array of all possible n-nucleotide oligomers (n-mers) to identify n-mers present in an unknown DNA sequence. Computational approaches can then be used to assemble the complete sequence. As a validation of this concept, the sequences of three DNA fragments, 343 base pairs in length, were determined with octamer oligonucleotides. Possible applications of SBH include physical mapping (ordering) of overlapping DNA clones, sequence checking, DNA fingerprinting comparisons of normal and disease-causing genes, and the identification of DNA fragments with particular sequence motifs in complementary DNA and genomic libraries. The SBH techniques may accelerate the mapping and sequencing phases of the human genome project.

Animals↗
PubMed1989

Interferons as gene activators. Indications for repeated gene duplication during the evolution of a cluster of interferon-activatable genes on murine chromosome 1.

We have described earlier a gene cluster, including at least six interferon-activatable genes closely linked to the erythroid alpha spectrin locus and the serum amyloid P-component locus on murine chromosome 1. Here, we report that sequences of three genes from the cluster (the 201, 202, and 204 genes) are very similar in a segment extending from at least 550 nucleotides upstream of the 3' end of the transcription initiation region to beyond the first exon intron border (96% similarity between the 202 and 204 genes and 89% similarity between the 201 and 204 genes). This region contains the following two types of interferon-responsive enhancers: a GA box and a Friedman Stark sequence. The proteins coded for by the 202 gene (51 kDa) and the 204 gene (72 kDa) are hydrophilic. The amino acids have been conserved in the two proteins in 47% of the sequence. Each protein includes two apparently contiguous, approximately 200-amino acid long segments with much sequence similarity (27% in the 202 protein and 34% in the 204 protein). These segments are preceded in the 204 protein only by a segment including four perfect and three imperfect repeats of a 7 amino acid sequence. These and other data suggest that the evolution of the gene cluster involved the duplication of a DNA segment generating a double length transcription unit and subsequent divergence and duplication of this unit giving rise to at least two interferon-activatable genes (the 202 and 204 genes).

Amino Acid Sequence↗
PubMed1989

Physical mapping of a family of interferon-activated genes, serum amyloid P-component, and alpha-spectrin on mouse chromosome 1.

This report defines genetic and physical relationships among alpha-spectrin (Spna-1), serum amyloid P-component (Sap), and a family of interferon-activated genes, provisionally designated Ifi202, Ifi203, and Ifi204. By linkage analysis using a large panel of interspecific backcross mice, Sap, Ifi202, and Ifi204 were shown to be tightly linked to Spna-1 on distal mouse chromosome 1. By pulsed field electrophoresis, a genomic restriction map of 6400 kb of distal mouse chromosome 1 was generated, linking genes encoding Sap, (Ifi202, Ifi203, Ifi204), and Spna-1 in that order within 450-1000 kb (where the genes within brackets were not ordered). The interferon-activated genes Ifi202, Ifi203, and Ifi204 were linked within 75-150 kb. Furthermore, genes transcriptionally activated by cytokines, namely Sap, Ifi202, Ifi203, and Ifi204, were located within 450 kb. These studies suggest the possibility that selective pressure may maintain in physical proximity gene clusters which are under coordinate transcriptional control.

Animals↗
PubMed1989

Interferons as gene activators: a cluster of six interferon-activatable genes is linked to the erythroid alpha-spectrin locus on murine chromosome 1.

Several interferon-activatable murine genes were mapped to murine chromosomes by hybridizing cDNA probes to Southern blots of genomic DNA samples from a panel of mouse-hamster somatic cell hybrid lines. The 12 gene is located on chromosome 12 and it specifies a 3.6-kb mRNA. The 204 gene (specifying a 2.5-kb mRNA), and three genes of the 203 gene family (hybridizing to five mRNAs of sizes between 2 and 4.5 kb), together with the 202 gene (specifying a 2-kb mRNA) are located on murine chromosome 1. By restriction fragment length polymorphism analysis of DNA samples prepared from a panel of recombinant inbred mouse lines (C57BL/6J D DBA/2J) and from 85 [C3H/HeJ-gld/gld x Mus spretus) F1 X C3H/HeJ-gld/gld] backcross mice we established a close linkage of the 202, 203, and 204 genes to the erythroid alpha-spectrin gene (Spna-1) on distal murine chromosome 1. Cosmids containing the 202, 203, and 204 genes were isolated from a library derived from AKR mouse DNA. Southern blot analysis of such cosmids revealed: (a) hybridization of a partial 203 cDNA to three genes of the 203 gene family; (b) cross-hybridization of the 202 and 204 genes with one another and with a third gene (designated as 201 gene), and (c) a close linkage of genes of the 203 family with the 201, 202, and 204 genes. These results indicate the existence of a cluster of at least six closely linked, interferon-activatable genes on distal murine chromosome 1 in the vicinity of the Spna-1 locus and also of the Minor lymphocyte stimulating locus (Mlsa).

Animals↗
PubMed1988

Interferons as gene activators: close linkage of two interferon-activatable murine genes.

Previously we have identified a mouse genomic clone (clone 5) which specifies the 5' flanking region and the 5' terminal exon of an interferon-activatable gene (202 gene). Here, we show that about 5 kb upstream from this flanking region in clone 5 there occurs a 3' terminal region of a second interferon-activatable gene (203 gene). The two genes are transcribed in the same direction. Segments from the 203 gene can be hybridized to a set of five interferon-inducible RNAs. The 203 mRNAs are induced about 15-fold in interferon-treated Ehrlich ascites tumor cells.

Animals↗