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Biomedical subjects

K Elliston

Publications and source records attributed to K Elliston.

8 recordsLinked to original sources
PubMed2004

Inferring gene regulatory networks from raw data--a molecular epistemics approach.

Biopathways play an important role in the functional understanding and interpretation of gene function. In this paper we present the results of an iterative algorithm for automatically generating gene regulatory networks from raw data. The algorithm is based on an epistemics approach of conjecture (hypothesis formation) and refutation (hypothesis testing). These operations are performed on a matrix representation of the gene network. Our approach also provides a way of incorporating external biological knowledge into the model. This is done by pre-assigning portions of the matrix--which represent previously known background knowledge. This background knowledge helps make the results closer to a human's rendition of such networks. We illustrate our approach by having the computer replicate a gene regulatory network generated by human scientists at an academic lab.

Algorithms↗
PubMed1995

PROFILER: a tool for automatic searching of internally maintained databases.

A new application program, the BIOINFORMATICS PROFILER, is described which simplifies the analysis of new genome sequence information appearing on a daily basis. Control tasks are defined through an intuitive graphical user interface and are executed at user defined nightly intervals. Electronic mail is sent to indicate that search results have been found. All task output is presented to users in the form of hypertext (HTML), allowing easy browsing. Currently supported tasks include BLAST and FastA sequence searching, keyword based searching of network news articles and WAIS databases, examination of GenBank sequence entries using regular expressions and boolean operations and protein sequence motif searching.

Amino Acid Sequence↗
PubMed1994

The C-terminus of the B cell activator Oct-2 functions as an activation domain in yeast.

Oct-1 and Oct-2 are human transcriptional activators that bind to the same DNA element but activate distinct sets of genes. We expressed these factors in S. cerevisiae and observed greater than 5-fold stimulation of a lacZ reporter gene only with Oct-2. Transfer of the Oct-2 C-terminal domain onto either Oct-1 (Oct1.2) or a nonactivating DNA-binding domain from GAL4 created activators capable of greater than 15 and 10-fold stimulation of activity, respectively. Thus, the C-terminus of Oct-2 is sufficient to confer activation potential to nonactive DNA-binding fragments in yeast.

B-Lymphocytes↗
PubMed1994

Carboxyl terminus of inducible nitric oxide synthase. Contribution to NADPH binding and enzymatic activity.

Cloning of a nitric oxide synthase (NOS) from RAW 264.7 mouse macrophages (Xie, Q.-w., Cho, H. J., Calaycay, J., Mumford, R. A., Swiderek, K. M., Lee, T. D., Ding, A., Troso, T., and Nathan, C. (1992) Science 256, 225-228) yielded two sets of cDNA: one with a longer coding region of 1144 amino acids, whose sequence matched that of the purified protein, and another with a shorter coding region of 1122 amino acids, in which the last 10 carboxyl-terminal amino acids differed completely from those of the long form. We have now found that the short form lacks NOS activity. To determine the basis of this defect, we prepared recombinant chimeric, deletional, and point mutants of the long and short NOS variants, monitored their expression by immunoblot, and tested their enzymatic activity. By itself, lack of the 22-carboxyl-terminal residues of the long form NOS was scarcely consequential. Mutation of Phe1122, the only aromatic residue within one of the longest conserved regions shared by all NOSs of reported sequence, reduced enzymatic activity by 41%. Deletion of 23 carboxyl-terminal amino acids (including Phe1122) reduced activity by 71%. Further loss of Ile1121, another completely conserved residue, reduced activity by 95%, and with the deletion of the rest of the conserved region, NOS activity was undetectable. Normal dimerization and binding of heme and calmodulin by the short variants militated against distortions of tertiary structure affecting the amino-terminal half or middle portion of the protein. In contrast, the short variants were deficient in binding to NADPH, as predicted by a model of tertiary structure based on that of spinach ferredoxin-NADP+ reductase. This is the first demonstration that the carboxyl terminus of NOS is a functionally critical region.

Amino Acid Oxidoreductases↗
PubMed1992

Cloning and expression of a cell surface receptor for advanced glycosylation end products of proteins.

Advanced glycosylation end products of proteins (AGEs) are nonenzymatically glycosylated proteins which accumulate in vascular tissue in aging and at an accelerated rate in diabetes. A approximately 35-kDa polypeptide with a unique NH2-terminal sequence has been isolated from bovine lung and found to be present on the surface of endothelial cells where it mediates the binding of AGEs (receptor for advanced glycosylation end product or RAGE). Using an oligonucleotide probe based on the amino-terminal sequence of RAGE, an apparently full-length cDNA of 1.5 kilobases was isolated from a bovine lung cDNA library. This cDNA encoded a 394 amino acid mature protein comprised of the following putative domains: an extracellular domain of 332 amino acids, a single hydrophobic membrane spanning domain of 19 amino acids, and a carboxyl-terminal domain of 43 amino acids. A partial clone encoding the human counterpart of RAGE, isolated from a human lung library, was found to be approximately 90% homologous to the bovine molecule. Based on computer analysis of the amino acid sequence of RAGE and comparison with databases, RAGE is a new member of the immunoglobulin superfamily of cell surface molecules and shares significant homology with MUC 18, NCAM, and the cytoplasmic domain of CD20. Expression of the RAGE cDNA in 293 cells allowed them to bind 125I-AGE-albumin in a saturable and dose-dependent manner (Kd approximately 100 nM), blocked by antibody to RAGE. Western blots of 293 cells transfected with RAGE cDNA probed with anti-RAGE IgG demonstrated expression of immunoreactive protein compared to its absence in mock-transfected cells. These results suggest that RAGE functions as a cell surface receptor for AGEs, which could potentially mediate cellular effects of this class of glycosylated proteins.

Albumins↗
PubMed1991

FKB1 encodes a nonessential FK 506-binding protein in Saccharomyces cerevisiae and contains regions suggesting homology to the cyclophilins.

FK 506, a powerful immunosuppressant that blocks allograft rejection by preventing T-cell activation, binds to an 11-kDa protein called the FK 506-binding protein (FKBP). Like cyclophilin, a cytosolic protein that binds another immunosuppressant, cyclosporin A, FKBP possesses peptidylprolyl cis-trans isomerase activity. We have isolated a genomic clone encoding the yeast FKBP (FKB1). The gene encodes a protein of 114 amino acids having a calculated Mr of 12,158. Disruption of the gene shows that FKB1 is not essential for growth. A search of translated nucleic acid data bases revealed bacterial FKBP homologs in Neisseria meningiditis and Pseudomonas aeruginosa. Comparison of the conserved amino acids in FKBP homologs with the conserved amino acids in the cyclophilins has revealed a region of similarity that we speculate to be a homologous domain related to the functional similarities of the two proteins.

Amino Acid Isomerases↗