APEX disease gene resequencing: mutations in exon 7 of the p53 tumor suppressor gene.

Detection of mutations in disease genes will be a significant application of genomic research. Methods for detecting mutations at the single nucleotide level are required in highly mutated genes such as the tumor suppressor p53. Resequencing of an individual patient's DNA by conventional Sanger methods is impractical, calling for novel methods for sequence analysis. Toward this end, an arrayed primer extension (APEX) method for identifying sequence alterations in primary DNA structure was developed. A two-dimensional array of immobilized primers (DNA chip) was fabricated to scan p53 exon 7 by single bases. Primers were immobilized with 200 microm spacing on a glass support. Oligonucleotide templates of length 72 were used to study individual APEX resequencing reactions. A template-dependent DNA polymerase extension was performed on the chip using fluorescein-labeled dideoxynucleotides (ddNTPs). Labeled primers were evanescently excited and the induced fluorescence was imaged by CCD. The average signal-to-noise ratio (S/N) observed was 30:1. Software was developed to analyze high-density DNA chips for sequence alterations. Deletion, insertion, and substitution mutations were detected. APEX can be used to scan for any mutation (up to two-base insertions) in a known region of DNA by fabricating a DNA chip comprising complementary primers addressing each nucleotide in the wild-type sequence. Since APEX is a parallel method for determining DNA sequence, the time required to assay a region is independent of its length. APEX has a high level of accuracy, is sequence-based, and can be miniaturized to analyze a large DNA region with minimal reagents.

Hallux amputation in combination with a lumbar sympathectomy for treatment of a non-healing ulceration in a patient with Buerger's disease.

Buerger's disease is a distal vascular occlusive disease primarily affecting those with a history of tobacco use. Treatment of digital pathology can be quite difficult as a result. This paper discusses a patient who developed an ulceration of the left hallux that did not respond to local wound care and antibiosis. A lumbar sympathectomy was performed in conjunction with a hallux amputation to promote distal vasodilation and enhance the patient's ability to heal.

Mutation detection by solid phase primer extension.

A mutation analysis method based upon a wild-type DNA sequence is presented. Oligonucleotides were utilized for primer extension by T7 DNA polymerase to discriminate between wild-type and mutant sequences in two solid phase approaches. 1. Oligonucleotides were annealed to an immobilized template, extended with fluorescent dideoxynucleotides (ddNTPs), and analyzed on an automated fluorescent DNA sequencer. The oligonucleotide length identified the known mutation site, and the fluorescence emission of the ddNTP identified the mutation. 2. Template DNA was annealed to an oligonucleotide array, extended with alpha-32P dNTPs, and analyzed with a Phosphor Imager. The grid position of the oligonucleotide identified the mutation site and the extended base identified the mutation.

Simulations of passive properties and action potential conduction in an idealized bullfrog atrial trabeculum.

This study investigates the properties of a distributed parameter model of an idealized trabeculum of cardiac muscle surrounded by a resistive-capacitive trabecular sheath. A mathematical approach is developed that permits the direct solution for the absolute potential in each medium [i.e., the intracellular (Vi), interstitial (Ve), and external (Vo) potentials), as opposed to obtaining solutions for the transmembrane potential V (where V identical to Vi-Ve). The mathematical description of the underlying individual cell is based upon quantitative whole-cell voltage-clamp measurements in bullfrog atrial myocytes. "Reduced" or "simplified" cell membrane models that lack the complete complement of transmembrane currents are compared with regard to their accuracy in representing the root, upstroke, and plateau regions of the propagated action potential in the complete model. The results show that a reduced cell membrane model must contain the sodium current INa, calcium current ICa, and background-rectifying K+ current IK1. A cell membrane model that contains a linear background K+ current IL instead of IK1 results in much poorer approximation to the upstroke, plateau, and conduction velocities of an action potential. The effects of varying the resistive-capacitive parameters of the trabecular sheath on both the passive properties (the time and space constants and the input resistance) and conduction parameters (time and space constants of the foot and conduction velocity of the action potential) of the trabeculum are also investigated. These simulations show that electrical activity within the trabeculum is much more sensitive to variations in the resistive component than in the capacitive component of the sheath. The trabecular sheath reduces the extracellular resistance seen by the cell by shunting current away from highly resistive interstitial medium into the volume conductor medium, which is of low resistance, and thereby increases conduction velocity. Finally, the addition of the cholinergic neurotransmitter acetylcholine to the extracellular medium reduces both the space constant of the trabeculum and the conduction velocity of propagated electrical activity.

A model of beta-adrenergic effects on calcium and potassium current in bullfrog atrial myocytes.

A model of beta-adrenergic and muscarinic cholinergic effects on the bullfrog atrial myocyte has been developed to simulate the dose-dependent effects of isoprenaline (Iso) on the action potential duration (APD); i.e., low doses of Iso lengthen the APD, whereas high doses shorten the APD. In this model, the reduction in APD is the result of 1) calcium-dependent inactivation of calcium current (ICa) resulting from the enhancement of ICa by Iso and 2) an enhancement of potassium current (IK) due to both an Iso-induced increase in the rate of activation of IK and an increase in peak action potential height. The effect of acetylcholine (ACh) is simulated by a reduction in the Iso-induced increase in ICa and IK through a reduction in relative adenosine 3',5'-cyclic monophosphate concentration ([cAMP]), as well as activation of the ACh-sensitive potassium current. At low [Iso] levels in the presence of a high [ACh], the muscarinic cholinergic effects dominate the beta-adrenergic change. However, for a large [Iso] and a small [ACh], this pattern of changes in transmembrane currents is different; in this case the model predicts that ACh can actually increase APD.

A model of the phase-sensitivity of the pacemaking cell in the bullfrog heart.

In this study, mathematical models of the bullfrog sinus venosus (SV) pacemaker cell (Rasmusson et al., 1990, Am. J. Physiol. 259, H352-H369) and the ACh-sensitive K+ channel (Shumaker et al., 1990, Biophys. J. 57, 567-576) are combined to simulate the response of the SV myocyte to brief hyperpolarizing currents or acetylcholine (ACh) pulses. These simulations provide an ionic basis for the interpretation of the response of this pacemaker cell to either single perturbation or periodic stimuli. The model predicts that the effects of ACh stimulation on the pacemaker cycle length are dependent both on the phase and temporal characteristics of the [ACh] waveform. For example, the simulations show that (1) although ACh normally has an inhibitory effect on the pacemaker model, for cases where the rise time and duration of the [ACh] waveform are sufficiently brief, ACh can paradoxically accelerate the beat in which a single stimulus is given; (2) the SV pacemaker normally exhibits type 1 (odd) phase-resetting in response to ACh delivery, however type 0 (even) phase-resetting behavior may be exhibited when the [ACh] waveform is large enough and has a very fast rise time; and (3) the SV pacemaker may become phase-locked to a repetitive ACh stimulus applied with either a constant period or coupling interval. In the latter case, this entrainment phenomenon has implications for the control of the cardiac pacemaker by a neural oscillator (e.g. located in the medullary cardiovascular control center) which provides input to the pacemaker cell via the vagus nerve. In these regions of capture, repetitive ACh stimulation produces a well-known paradoxical accelerative effect on the SV pacemaker cell, similar to that seen in a variety of other species.

A model of the muscarinic receptor-induced changes in K(+)-current and action potentials in the bullfrog atrial cell.

A model is formulated for characterizing the behavior of the acetylcholine (ACh)-sensitive K+ membrane channel (muscarinic channel) in bullfrog atrial myocytes. Parameters of the muscarinic current model are chosen in fit available data from the literature on bullfrog atrial myocytes (3, 4, 45). This model is subsequently incorporated into a large mathematical model of the bullfrog myocyte that is based on quantitative whole-cell voltage clamp data (40). Simulations are conducted on the active atrial cell model in bathing media containing ACh at different concentrations to explore the effect of this muscarinic channel on the electrical behavior of the myocyte. The model predicts a progressive shortening of the action potential with increasing [ACh], as well as an indirect influence of the muscarinic K+ current on the other membrane currents of the atrial cell. Interpretation of the simulation results provides suggestions for the probable mechanisms underlying the shortening of the action potential due to activity of the muscarinic channel. Specifically, the model predicts that with an increase in ACh concentration: (a) the outward muscarinic current, IK,ACh(t), increases in magnitude but shortens in duration; (b) the calcium current, ICa(t), may increase in magnitude, but when it does so it decreases in duration compared with the control conditions; (c) the intracellular Ca2+ concentration [Ca2+]i waveform during the action potential decreases in both magnitude and duration. Because the contractile activity of the cell is controlled by the [Ca2+]i waveform, the model predicts a decrease in contractile strength with an increase in ACh concentration in the bathing medium; i.e., a negative inotropic effect.