Highly parallel SNP genotyping.
Explore the source record for details and available documents.
Alleles↗
Biomedical subjects
A Oliphant
Publications and source records attributed to A Oliphant.
Nitrogen deposition to and cycling in a deciduous forest.
The project described here seeks to answer questions regarding the role increased nitrogen (N) deposition is playing in enhanced carbon (C) sequestration in temperate mid-latitude forests, using detailed measurements from an AmeriFlux tower in southern Indiana (Morgan-Monroe State Forest, or MMSF). The measurements indicate an average atmosphere-surface N flux of approximately 6 mg-N m(-2) day(-1) during the 2000 growing season, with approximately 40% coming from dry deposition of ammonia (NH3), nitric acid (HNO3), and particle-bound N. Wet deposition and throughfall measurements indicate significant canopy uptake of N (particularly NH4+) at the site, leading to a net canopy exchange (NCE) of -6 kg-N ha(-1) for the growing season. These data are used in combination with data on the aboveground C:N ratio, litterfall flux, and soil net N mineralization rates to indicate the level of potential perturbation of C sequestration at this site.
Ammonia↗
(4-Piperidin-1-yl)phenyl amides: potent and selective human beta(3) agonists.
In search of potent and selective human beta(3) agonists as potential drugs for the treatment of human obesity and type II diabetes, a series of (4-piperidin-1-yl)phenyl amides was prepared and evaluated for their biological activity on the human beta(3)-adrenergic receptor. The leucine derivative 26e and the reverse amide 33b were found to be the two most potent and selective compounds in this study. With EC(50) values of 0.008 and 0.009 microM, respectively, at the beta(3) receptor, nearly completely abolished intrinsic activity at either the beta(1) or beta(2) receptor, and significant thermogenesis effects on human beta(3)-adrenergic receptor transgenic mice, 26e and33b are among the most potent and selective human beta(3) agonists known to date.
Adrenergic beta-Agonists↗
2,4-Thiazolidinediones as potent and selective human beta3 agonists.
Methylsulfonamide substituted 2,4-thiazolidinedione 22c is a potent (EC50=0.01 microM, IA=1.19) and selective (more than 110-fold over beta1 and beta2 agonist activity) beta3 agonist. This compound has also been proven to be active and selective in an in vivo mode.
Adrenergic beta-3 Receptor Agonists↗
Novel (4-piperidin-1-yl)-phenyl sulfonamides as potent and selective human beta(3) agonists.
A series of novel (4-piperidin-1-yl)-phenyl sulfonamides was prepared and evaluated for their biological activity on the human beta(3)-adrenergic receptor (AR). Replacement of the 3,4-dihydroxyl group of the catechol moiety with 4-hydroxyl-3-methyl sulfonamide on the left-hand side of the compounds resulted in a number of potent full agonists at the beta(3) receptor. Modification of the right-hand side of the compounds by incorporation of a free carboxylic acid resulted in a few potent human beta(3) agonists with low affinities for beta(1)- and beta(2)-ARs. N-Alkyl substitution on the 4-piperidin-1-yl-phenylamine further increased the beta(3) potency while maintaining the selectivity. For example, sulfonamide 48 is a potent full beta(3) agonist (EC(50)=0.004 microM, IA=1.0) with > 500-fold selectivity over beta(1)- and beta(2)-ARs.
Adrenergic beta-3 Receptor Agonists↗
BRCA1 sequence analysis in women at high risk for susceptibility mutations. Risk factor analysis and implications for genetic testing.
CONTEXT: A mutation in the BRCA1 gene may confer substantial risk for breast and/or ovarian cancer. However, knowledge regarding all possible mutations and the relationship between risk factors and mutations is incomplete. OBJECTIVES: To identify BRCA1 mutations and to determine factors that best predict presence of a deleterious BRCA1 mutation in patients with breast and/or ovarian cancer. DESIGN: A complete sequence analysis of the BRCA1 coding sequence and flanking intronic regions was performed in 798 women in a collaborative effort involving institutions from the United States, Italy, Germany, Finland, and Switzerland. PARTICIPANTS: Institutions selected 798 persons representing families (1 person for each family) thought to be at elevated a priori risk of BRCA1 mutation due to potential risk factors, such as multiple cases of breast cancer, early age of breast cancer diagnosis, and cases of ovarian cancer. No participant was from a family in which genetic markers showed linkage to the BRCA1 locus. MAJOR OUTCOME MEASURES: Sequence variants detected in this sample are presented along with analyses designed to determine predictive characteristics of those testing positive for BRCA1 mutations. RESULTS: In 102 women (12.8%), clearly deleterious mutations were detected. Fifty new genetic alterations were found including 24 deleterious mutations, 24 variants of unknown significance, and 2 rare polymorphisms. In a subset of 71 Ashkenazi Jewish women, only 2 distinct deleterious mutations were found: 185delAG in 17 cases and 5382insC in 7 cases. A bias in prior reports for mutations in exon 11 was revealed. Characteristics of a patient's specific diagnosis (unilateral or bilateral breast cancer, with or without ovarian cancer), early age at diagnosis, Ashkenazi Jewish ethnicity, and family history of cancer were positively associated with the probability of her carrying a deleterious BRCA1 mutation. CONCLUSIONS: Using logistic regression analysis, we provide a method for evaluating the probability of a woman's carrying a deleterious BRCA1 mutation for a wide range of cases, which can be an important tool for clinicians as they incorporate genetic susceptibility testing into their medical practice.
Breast Neoplasms↗
The sequence of the Mycoplasma arthritidis superantigen, MAM: identification of functional domains and comparison with microbial superantigens and plant lectin mitogens.
Mycoplasma arthritidis, an agent of chronic proliferative arthritis of rodents, secretes a potent soluble superantigen, MAM, that is active for both murine and human T and B lymphocytes. We now report the complete nucleotide and amino acid sequence of MAM and show it to be distinct from other proteins and not closely related phylogenetically to other superantigens. Two functional domains on MAM are identified based on the ability of peptides encompassing these regions to inhibit lymphocyte proliferation by the intact MAM molecule. One of these domains shares short sequences or epitopes with other microbial superantigens. The second domain contains the consensus legume lectin motif-beta, which is important for T cell activation by concanavalin (Con) A. MAM and Con A peptides containing this motif are functionally cross reactive, suggesting a novel secondary pathway for T cell activation by MAM.
Amino Acid Sequence↗
Hypomethylated sequences: characterization of the duplicate soybean genome.
Soybean is believed to be a diploidized tetraploid generated from an allotetraploid ancestor. In this study, we used hypomethylated genomic DNA as a source of probes to investigate the genomic structure and methylation patterns of duplicated sequences. Forty-five genomic clones from Phaseolus vulgaris and 664 genomic clones from Glycine max were used to examine the duplicated regions in the soybean genome. Southern analysis of genomic DNA using probes from both sources revealed that greater than 15% of the hypomethylated genomic regions were only present once in the soybean genome. The remaining ca. 85% of the hypomethylated regions comprise duplicated or middle repetitive DNA sequences. If only the ratio of single to duplicate probe patterns is considered, it appears that 25% of the single-copy sequences have been lost. By using a subset of probes that only detected duplicated sequences, we examined the methylation status of the homeologous genomes with the restriction enzymes MspI and HpaII. We found that in all cases both copies of these regions were hypomethylated, although there were examples of low-level methylation. It appears that duplicate sequences are being eliminated in the diploidization process. Our data reveal no evidence that duplicated sequences are being "silenced" by inactivation correlated with methylation patterns.
DNA, Plant↗
Chromosome 17q linkage studies of 18 Utah breast cancer kindreds.
In this paper we present linkage results from the analysis of 18 Utah breast cancer kindreds, for three 17q markers. Four kindreds had LOD scores greater than 1.0 for at least one of the marker loci. One of these kindreds has a LOD score of 6.07 with D17S579, and we believe it to be the most informative 17q family reported to date. Among the kindreds which appear unlinked to 17q were an early-onset breast cancer family, a large breast-ovarian family, and a kindred with mixed age at onset. Analysis of individual recombinants in the linked families localizes the BRCA1 gene between THRA1 and D17S579 (Mfd188). A comparison of the Cancer and Steroid Hormone Study (CASH) model and a model which assumes a rare dominant susceptibility locus with low penetrance and no phenocopies stresses the difficulties in assessing linkage if the assumptions of the CASH model in terms of age at onset of breast cancer are not appropriate for the BRCA1 locus. A hypothetical breast cancer pedigree is used to calculate gene carrier probabilities under the CASH model, thereby illustrating some of our concerns regarding the use of this model to detect and exclude 17q linkage in breast cancer families.
Adult↗
Genetic linkage map of human chromosome 7 with 63 DNA markers.
High-density genetic maps of individual human chromosomes will permit accurate localization of disease-associated genes and provide signposts that will be useful in the construction of physical maps. We have constructed a genetic map of chromosome 7 with 63 polymorphic DNA markers by using segregation data from 23 three-generation families and recently developed multilocus linkage-analysis techniques. The map spans 250 centimorgans in females and 170 centimorgans in males, with much of the difference being concentrated in a few intervals. The density and informativeness of the markers are such that there is a high probability of detecting linkage to any disease gene on this chromosome for which 20 phase-known meioses are available.
Chromosome Mapping↗
A second type II restriction endonuclease from Thermus aquaticus with an unusual sequence specificity.
A type II restriction endonuclease activity free of TaqI was prepared from Thermus Aquaticus YT. The fraction contains two endonucleolytic components with apparently different specificities, however the major activity is sufficiently dominant to allow partial digestion analysis of the position of recognition sites. A precise determination of the location of cleavage sites in pBR322 DNA and a computer-aided search for regions of homology in the vicinity of the cut sites indicate that this enzyme recognizes the nonpalindromic sequences GACCGA or CACCCA. Other related sequences are not cleaved, in particular, GACCCA and CACCGA, indicating that the enzyme requires the identity of nucleotides in the first and fifth positions, a type of specificity that has not been previously reported. The position of cleavage is located outside of the site and is represented as: (Formula: see text).
Base Sequence↗