The gender-specific apolipoprotein E genotype influence on the distribution of plasma lipids and apolipoproteins in the population of Rochester, MN. III. Correlations and covariances.

The gender-specific influence that the apolipoprotein E (ApoE) polymorphism has on the correlations and covariances between pairs of nine plasma lipid and apolipoprotein traits (total cholesterol; in triglycerides; high-density-lipoprotein cholesterol; apolipoproteins AI, AII, B, CII, lnCIII, and lnE) was studied in 507 unrelated individuals representative of the adult population of Rochester, MN. Analyses are presented separately for females and males. The Apo E polymorphism had a significant influence on a large number (10 of 36) of correlations and covariances in females and on a small number (3 of 36) in males. The contribution of allelic variation in the Apo E gene to the definition of multivariate measures of the 36-dimensional correlation structure was evaluated. The influence of Apo E genotype on correlation structure was gender dependent. These findings were used to demonstrate how heterogeneity of risk-factor correlations and covariances among genotype-gender subgroups of the population at large may influence the evaluation of risk of coronary artery disease.     

Echocardiographic assessment and percutaneous closure of multiple atrial septal defects

Percutaneous coronary intervention can be associated with distal embolization of thrombotic material causing myocardial necrosis and infarction. We discuss the role of intravascular imaging to guide the use of a distal protection device by describing the outcome of a young woman presenting with non-ST elevation myocardial infarction. Coronary angiography demonstrated an isolated minor stenosis in the proximal left anterior descending coronary artery with slight haziness beyond the lesion. Intravascular ultrasound confirmed an extensive thrombus overlying a bulky atherosclerotic plaque. A distal filter wire was therefore successfully used to reduce the risk of distal embolization. The use of intravascular ultrasound in patients presenting with acute coronary syndrome may reveal large thrombi that are difficult to image using conventional angiographic techniques. Intravascular ultrasound can therefore be used as a tool to select lesions requiring distal protection.     

Myelination in the chorda tympani of the postnatal rat: a quantitative electron microscope study

We determined the course of myelination of the chorda tympani in rats aged from 4- to 30-days-old, the interval of the most rapid developmental changes in neurophysiological taste responses and behavioral discrimination among chemical stimuli. The overall number of axons in rats aged from 16- to 30-days-old and in mature 120-day-old animals were the same and averaged 1,500. By 30 days, rats had 80% of the total number of myelinated axons observed in adults, but the average thickness of the myelin sheath per neuron and the proportion of the total cross-sectional area that were only about 60% of adult values. Observed increases in myelination closely parallel decreasing response latencies of single chorda tympani fibers to tongue stimulation with salts.     

Mechanisms of specificity in protein phosphorylation

A typical protein kinase must recognize between one and a few hundred bona fide phosphorylation sites in a background of approximately 700,000 potentially phosphorylatable residues. Multiple mechanisms have evolved that contribute to this exquisite specificity, including the structure of the catalytic site, local and distal interactions between the kinase and substrate, the formation of complexes with scaffolding and adaptor proteins that spatially regulate the kinase, systems-level competition between substrates, and error-correction mechanisms. The responsibility for the recognition of substrates by protein kinases appears to be distributed among a large number of independent, imperfect specificity mechanisms.     

Simple, realistic models of complex biological processes: Positive feedback and bistability in a cell fate switch and a cell cycle oscillator

Here we review some of our work over the last decade on Xenopus oocyte maturation, a cell fate switch, and the Xenopus embryonic cell cycle, a highly dynamical process. Our approach has been to start with wiring diagrams for the regulatory networks that underpin the processes; carry out quantitative experiments to describe the response functions for individual legs of the networks; and then construct simple analytical models based on chemical kinetic theory and the graphical rate-balance formalism. These studies support the view that the all-or-none, irreversible nature of oocyte maturation arises from a saddle-node bifurcation in the regulatory system that drives the process, and that the clock-like oscillations of the embryo are built upon a hysteretic switch with two saddle-node bifurcations. We believe that this type of reductionistic systems biology holds great promise for understanding complicated biochemical processes in simpler terms.     

Proteinase-activated receptor-2 mediated inhibition of TNFα-stimulated JNK activation — A novel paradigm for Gq/11 linked GPCRs

In this study we examined the potential for PAR₂ and TNFα to synergise at the level of MAP kinase signalling in PAR₂ expressing NCTC2544 cells. However, to our surprise we found that activation of PAR₂ by trypsin or the specific activating peptide SLIGKV-OH strongly inhibited both the phosphorylation and activity of JNK. In contrast neither p38 MAP kinase nor ERK activation was affected although TNFα stimulated IκBα loss was partially reversed. The inhibitory effect was not observed in parental cells nor in cells expressing PAR₄, however inhibition was reversed by pre-incubation with the novel PAR₂ antagonist K14585, suggesting that the effect is specific for PAR₂ activation. SLIGKV-OH was found to be more potent in inhibiting TNFα-induced JNK activation than in stimulating JNK alone, suggesting agonist-directed signalling. The PKC activator PMA, also mimicked the inhibitory effect of SLIGKV-OH, and the effects of both agents were reversed by pre-treatment with the PKC inhibitor, GF109203X. Furthermore, incubation with the novel G_q/11 inhibitor YM25480 also reversed PAR₂ mediated inhibition. Activation of PAR₂ was found to disrupt TNFR1 binding to RIP and TRADD and this was reversed by both GF109203X and YM25480. A similar mode of inhibition observed in HUVECs through PAR₂ or P2Y2 receptors demonstrates the potential of a novel paradigm for GPCRs linked to G_q/11, in mediating inhibition of TNFα-stimulated JNK activation. This has important implications in assessing the role of GPCRs in inflammation and other conditions.     

Structural Models for Interactions between the 20S Proteasome and Its PAN/19S Activators

Proteasome activity is regulated by sequestration of its proteolytic centers in a barrel-shaped structure that limits substrate access. Substrates enter the proteasome by means of activator complexes that bind to the end rings of proteasome α subunits and induce opening of an axial entrance/exit pore. The PA26 activator binds in a pocket on the proteasome surface using main chain contacts of its C-terminal residues and uses an internal activation loop to trigger gate opening by repositioning the proteasome Pro-17 reverse turn. Subunits of the unrelated PAN/19S activators bind with their C termini in the same pockets but can induce proteasome gate opening entirely from interactions of their C-terminal peptides, which are reported to cause gate opening by inducing a rocking motion of proteasome α subunits rather than by directly contacting the Pro-17 turn. Here we report crystal structures and binding studies of proteasome complexes with PA26 constructs that display modified C-terminal residues, including those corresponding to PAN. These findings suggest that PA26 and PAN/19S C-terminal residues bind superimposably and that both classes of activator induce gate opening by using direct contacts to residues of the proteasome Pro-17 reverse turn. In the case of the PAN and 19S activators, a penultimate tyrosine/phenylalanine residue contacts the proteasome Gly-19 carbonyl oxygen to stabilize the open conformation.     

Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy

The noninvasive character of NMR spectroscopy, combined with the sensitivity of the chemical shift, makes it ideally suited to investigate the conformation, binding events and dynamics of macromolecules inside living cells. These 'in-cell NMR' experiments involve labeling the macromolecule of interest with a nonradioactive but NMR-active isotope (15N or 13C). Cellular samples are prepared either by selectively overexpressing the protein in suitable cells (e.g., bacterial cells grown on isotopically labeled media), or by injecting isotopically labeled proteins directly into either cells or cell extracts. Here we provide detailed protocols for in-cell NMR experiments in the prokaryotic organism Escherichia coli, as well as eukaryotic cells and extracts employing Xenopus laevis oocytes or egg extracts. In-cell NMR samples with proteins overexpressed in E. coli can be produced within 13-14 h. Preparing Xenopus oocyte samples for in-cell NMR experiments takes 6-14 h depending on the oocyte preparation scheme and the injection method used.