PubMed Health⌕ Search

Biomedical subjects

J Pontius

Publications and source records attributed to J Pontius.

4 recordsLinked to original sources
PubMed2001

A radiation hybrid map of mouse genes.

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, the Medical Research Council UK Mouse Genome Centre, and the National Center for Biotechnology Information. The map contains 11,109 genes, screened against the T31 RH panel and positioned relative to a reference map containing 2,280 mouse genetic markers. It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome.

Animals↗
PubMed1996

Deviations from standard atomic volumes as a quality measure for protein crystal structures.

Standard ranges of atomic and residue volumes are computed in 64 highly resolved and well-refined protein crystal structures using the classical Voronoi procedure. Deviations of the atomic volumes from the standard values, evaluated as the volume Z-scores, are used to assess the quality of protein crystal structures. To score a structure globally, we compute the volume Z-score root mean square deviation (Z-score rms), which measures the average magnitude of the volume irregularities in the structure. We find that the Z-score rms decreases as the resolution and R-factor improve, consistent with the fact that these improvements generally reflect more accurate models. From the Z-score rms distribution in structures with a given resolution or R-factor, we determine the normal limits in Z-score rms values for structures solved at that resolution or R-factor. Structures whose Z-score rms exceeds these limits are considered as outliers. Such structures also exhibit unusual stereochemistry, as revealed by other analyses. Absolute Z-scores of individual atoms are used to identify problems in specific regions within a protein model. These Z-scores correlate fairly well with the atomic B-factors, and atoms having absolute Z-scores > 3, occur at or near regions in the model where programs such as PROCHECK identify unusual stereochemistry. Atomic volumes, themselves not directly restrained in crystallographic refinement, can thus provide an independent, rather sensitive, measure of the quality of a protein structure. The volume-based structure validation procedures are implemented in the program PROVE (PROtein Volume Evaluation), which is accessible through the World Wide Web.

Amino Acid Sequence↗
PubMed1988

In vitro effect of fresh frozen plasma on the activated coagulation time in patients undergoing cardiopulmonary bypass.

The in vitro effect of fresh frozen plasma (FFP) on the whole blood activated coagulation time (ACT) was examined in 18 patients undergoing cardiopulmonary bypass (CPB) during coronary artery bypass graft surgery. The addition of FFP to whole blood in vitro, after systemic heparinization, significantly prolonged the ACT from 451 +/- 21 seconds (mean +/- SE) to 572 +/- 41 seconds (P less than 0.05). There was no significant correlation between the plasma antithrombin III activity and the prolongation in ACT after systemic heparinization, with or without addition of FFP. The addition of FFP to whole blood in three of the six patients who exhibited heparin resistance (ACT less than 400 seconds after administration of 350 unit/kg heparin) did not prolong the ACT to greater than 400 seconds. These observations suggest that infusion of FFP will further prolong the ACT after heparin administration in most patients including some with initial heparin resistance.

Adult↗