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Biomedical subjects

J M Hubbard

Publications and source records attributed to J M Hubbard.

8 recordsLinked to original sources
PubMed1993

Modeling study of antibody combining sites to (alpha 1-6)dextrans. Predictions of the conformational contribution of VL-CDR3 and J kappa segments to groove-type combining sites.

The shuffling of the V kappa-Ox1 light chain joined to J kappa 4 of J kappa 5 instead of J kappa 2 reduced or abolished antigen binding of three groove-type anti-(alpha 1-6)dextran monoclonal antibodies, raising questions as to the structural roles of J kappa in antibody combining sites. The J kappa 4 light chain used contains Pro95A at the V kappa-Ox1-J kappa 4 junction, as well as a Phe to Ile substitution at the beginning of this J kappa 4 segment. To predict whether the defect in antigen binding is a consequence of the J kappa replacement, the Pro insertion or the Phe to Ile substitution, model-building studies were performed. As shown by the surface representation of antibody combining sites, the models with length variation in the VL-CDR3 loop by only 1 residue altered the shape of the combining site dramatically; whereas those with replacement of J kappa or having amino acid substitutions in VL-CDR3 affect the combining site less extensively. A distinct loop configuration of VL-CDR3 appears in models having either a Pro, Gly, or Ala insertion at position 95A. These results indicate that the length of VL-CDR3 is crucial for its loop conformation and may, therefore, have played a major role in abolishing dextran binding activity of the J kappa 4 variants. The potential of V kappa-Ox1 genes in generating conformational diversity in the loop of VL-CDR3 and its influence in forming different combining sites are discussed.

Amino Acid Sequence↗
PubMed1991

Computer modeling 16 S ribosomal RNA.

A three-dimensional structure for 16 S RNA has been produced with a computer protocol that is not dependent on human intervention. This protocol improves upon traditional modeling techniques by using distance geometry to fold the molecule in an objective and reproducible fashion. The method is based on the secondary structure of RNA and treats the molecule as a set of double-stranded helices that are linked by flexible single-strands of variable length. Data derived from chemical cross-linking studies of 16 S RNA and tertiary phylogenetic relationships provide the constraints used to fold the molecule into a compact three-dimensional form. Possibly subjective evaluation of the input data are transformed into verifiable quantitative parameters. Relationships based on general locations within the 30 S subunit or on protein-RNA interactions have been specifically excluded. The resolution of the model exceeds that of electron micrographs and approaches that obtained in preliminary X-ray crystal structures. The model size of 245 x 190 x 140 A is compatible with that of the 30 S subunit as determined by electron microscopy. The volume of the model is 1.87 x 10(6) A which is similar to that of the small subunit in a preliminary X-ray crystal structure. The radius of gyration of the model structure of 76 A is intermediate to that seen for partially denatured and fully folded 16 S RNA. Computer graphics are used to display the results in a manner that maximizes the opportunities for human visual interpretation of the models. A format for displaying the structures has been developed that will make it possible for researchers who have not devoted themselves to ribosomal modeling to comprehend and make use of the information that the models embody. On this basis the computer-generated models are compared with models developed by other researchers and with structural data not included in the folding parameter data set.

Base Sequence↗
PubMed1991

Predicting the three-dimensional folding of transfer RNA with a computer modeling protocol.

We have developed a computer modeling protocol that can be used to predict the three-dimensional folding of a ribonucleic acid on the basis of limited amounts of secondary and tertiary data. This protocol extends the use of distance geometry beyond the domain of NMR data in which it is usually applied. The use of this algorithm to fold the molecule eliminates operator subjectivity and reproducibly predicts the overall dimensions and shape of the transfer RNA molecule. By use of a replacement pseudoatom set based on helical substructures, a series of transfer RNA foldings have been completed that utilize only the primary structure, the phylogenetically deduced secondary structure, and five long-range interactions that were determined without reference to the crystal structure. In a control set of foldings, all the interactions suspected to exist in 1969 have been included. In all cases, the modeling process consistently predicts the global arrangement of the helical domains and to a lesser extent the general path of the backbone of transfer RNA.

Computer Simulation↗
PubMed1991

Exposing patients with chronic, stable, exertional angina to placebo periods in drug trials.

Because the safety of withholding standard therapy and enrolling patients with stable angina in placebo-controlled trials is not known, we identified all events leading to dropout from trials of 12 antianginal drugs submitted in support of new drug applications to the US Food and Drug Administration. Persons who dropped out of the trials were classified as cause due to adverse cardiovascular events or other causes without knowledge of drug assignment. There were 3161 subjects who entered any randomized, double-blind phase of placebo-controlled protocols; 197 (6.2%) withdrew because of cardiovascular events. There was no difference in risk of adverse events between drug and placebo groups. A prospectively defined subgroup analysis showed that groups who received calcium antagonists were at an increased risk of dropout compared with placebo groups (P = .04), primarily because of a disproportionate number of adverse events in studies of one drug. In conclusion, there were few adverse experiences associated with short-term placebo use. Withholding active treatment does not increase the risk of serious cardiac events.

Adrenergic beta-Antagonists↗
PubMed1990

The Hymenoptera venom study. III: Safety of venom immunotherapy.

One thousand four hundred ten (44%) of the 3236 subjects in the Hymenoptera venom study accepted venom immunotherapy (VIT). Time to maintenance averaged 95 days, and the largest number achieved maintenance (147 subjects, 10.4%) at day 56. Ninety-two percent of the treated subjects achieved maintenance, and 84% continued therapy, most subjects (91%) until the study was terminated. One hundred seventy-one subjects (12%) experienced 327 treatment systemic reactions (Srs). The incidence of pruritus and angioedema/urticaria was similar with mild, moderate, or severe SRs. The SR severity did not correlate with the severity of the most recent sting before entry into the Hymenoptera-venom study, the most severe historical sting SR, the most severe SR during venom skin tests, the total dose of venom, the degree of skin test reactivity, or the lowest concentration yielding a positive skin test. Most SRs occurred between 1 and 50 micrograms and at maintenance; honeybee or wasp venoms were most likely to produce SR. This study, the largest of its kind with the use of standardized extracts, demonstrates (1) that there was good compliance, (2) that various historical and diagnostic criteria did not predict SRs to VIT, (3) that SRs to VIT were most likely to occur between 1 and 50 micrograms and at maintenance, (4) that honeybee or wasp venoms were most likely to produce an SR, and (5) that VIT is relatively safe.

Animals↗
PubMed1982

Pursuit Meter II, a computer-based device for testing pursuit-tracking performance.

The Pursuit Meter II, a microcomputer-based device developed for the quantitative determination of human pursuit-tracking performance, is described. Computer-generated moving patterns are displayed on a high resolution color video monitor. For the subject the task is to attempt to superimpose a red line presented on the screen, the vertical location of which he controls with a steering device, over a blue line the computer generates as the problem. Both lines, each composed of 279 segments, are generated at the same rate, left to right on the monitor. The individual differences between the subject's response and the problem are summed and stored by the computer as an error score which correlates inversely to the subject's ability to perform the task. Three Pursuit Meter II problems were presented to 26 male college students. Our data demonstrated that different levels of performance to the problems resulted and that the Pursuit Meter II can be used to quantify human pursuit-tracking performance.

Computers↗
PubMedDate not supplied

Lack of correlation between plasma 4-hydroxyglutethimide and severity of coma in acute glutethimide poisoning. A case report and brief review of the literature.

Glutethimide poisoning is characterised by coma, anticholinergic poisoning syndrome, hypotension, and other complications. Previous studies have shown that the severity of intoxication does not correlate with plasma glutethimide concentrations in individual patients. Glutethimide is partly converted to 4-hydroxyglutethimide, a metabolite which accumulates in the plasma of humans, and which has been thought to contribute to coma after plasma glutethimide concentrations have fallen. We followed plasma concentrations of glutethimide and 4-hydroxyglutethimide in a man who overdosed with glutethimide. Plasma 4-hydroxyglutethimide concentrations did not correlate with the degree of coma in our patient, and actually rose as the patient awakened. Other studies also indicate that 4-hydroxyglutethimide may not play an important role in glutethimide poisoning.

Coma↗