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At least 19 recordsLinked to original sources
PubMed1989

Kinetic analysis of base substitution mutagenesis by transient misalignment of DNA and by miscoding.

We measured the insertion fidelity of DNA polymerases alpha and beta and yeast DNA polymerase I at a template site that was previously observed to yield a high frequency of T----G transversions when copied by DNA polymerase beta but not by the other two polymerases. The results provide direct biochemical evidence that base substitution errors by DNA polymerase beta can result from a dislocation mechanism governed by DNA template-primer misalignment. In contrast to DNA polymerase beta, neither Drosophila DNA polymerase alpha nor yeast DNA polymerase I appear to misinsert nucleotides by a dislocation mechanism in either the genetic or kinetic fidelity assays. Dislocation errors by DNA polymerase beta are characterized primarily by a substantial reduction in the apparent Km for inserting a "correct," but ultimately errant, nucleotide compared to the apparent Km governing direct misinsertion. For synthesis by DNA polymerase beta, dislocation results in a 35-fold increase in dCMP incorporation opposite template T (T----G transversion) and a 20-35-fold increase in dTMP incorporation opposite T (T----A transversion); these results are consistent with parallel genetic fidelity measurements. DNA polymerase beta also produces base substitution errors by direct misinsertion. Here nucleotide insertion fidelity results from substantial differences in both Km and Vmax for correct versus incorrect substrates and is influenced strongly by local base sequence.

Animals↗
PubMed1991

An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics.

An exonuclease-deficient mutant of T7 DNA polymerase was constructed and utilized in a series of kinetic studies on misincorporation and next correct dNTP incorporation. By using a synthetic oligonucleotide template-primer system for which the kinetic pathway for correct incorporation has been solved [Patel, S.S., Wong, I., & Johnson, K. A. (1991) Biochemistry (first of three papers in this issue)], the kinetic parameters for the incorporation of the incorrect triphosphates dATP, dCTP, and dGTP were determined, giving, respectively, kcat/Km values of 91, 23, and 4.3 M-1 s-1 and a discrimination in the polymerization step of 10(5)-10(6). The rates of misincorporation in all cases were linearly dependent on substrate concentration up to 4 mM, beyond which severe inhibition was observed. Competition of correct incorporation versus dCTP revealed an estimated Ki of approximately 6-8 mM, suggesting a corresponding kcat of 0.14s-1. Moderate elemental effects of 19-, 17-, and 34-fold reduction in rates were measured by substituting the alpha-thiotriphosphate analogues for dATP, dCTP, and dGTP, respectively, indicating that the chemistry step is partially rate-limiting. The absence of a burst of incorporation during the first turnover places the rate-limiting step at a triphosphate binding induced conformational change before chemistry. In contrast, the incorporation of the next correct triphosphate, dCTP, on a mismatched DNA substrate was saturable with a Km of 87 microM for dCTP, 4-fold higher than the Kd for the correct incorporation on duplex DNA, and a kcat of 0.025 s-1. A larger elemental effect of 60, however, suggests a rate-limiting chemistry step. The rate of pyrophosphorolysis on a mismatched 3'-end is undetectable, indicating that pyrophosphorolysis does not play a proofreading role in replication. These results show convincingly that the T7 DNA polymerase discriminates against the incorrect triphosphate by an induced-fit conformational change and that, following misincorporation, the enzyme then selects against the resultant mismatched DNA by a slow, rate-limiting chemistry step, thereby allowing sufficient time for the release of the mismatched DNA from the polymerase active site to be followed by exonucleolytic error correction.

DNA Replication↗
PubMed1978

Systolic time intervals in atrial fibrillation.

Forty patients with atrial fibrillation and 20 patients with congestive heart failure and sinus rhythm were studied. Patients were divided into two groups. Group A consisted of 20 patients with atrial fibrillation in whom systolic time intervals were measured. Twenty to 50 beats were analyzed. Five of the patients had high-fidelity measurements of left ventricular pressure simultaneous with determination of systolic time intervals. Analysis of the systolic time intervals for the entire group showed that the preejection period lengthened at faster heart rates and that the left ventricular ejection time was relatively constant at slower heart rates. This resulted in a progressive increase in the ratio of preejection period over left ventricular ejection time (PEP/LVET) as the heart rate increased. The rate of increase in PEP/LVET was minimal below a heart rate of 75 beats per minute. The increase in preejection period at faster heart rates is due to greater isovolumic developed pressure without a corresponding increase in left ventricular dp/dt. Group B consisted of 40 additional patients (20 with atrial fibrillation and 20 with sinus rhythm). In group B, the total electromechanical systole corrected for heart rate (QS2I) and the levels of digoxin in the blood were compared. The QS2I was significantly shorter in atrial fibrillation (497 +/- 5 msec vs 528 +/- 4 msec; P less than 0.01), while the levels of digoxin in the blood were identical (0.9 +/- 0.1 vs 1.0 +/- 0.1 ng/ml). The results of this study must be considered when systolic time intervals are to be employed in patients with atrial fibrillation.

Adult↗
PubMed1992

A DNA repair defect in a radiation-sensitive clone of a human bladder carcinoma cell line.

DNA repair was measured in an ionising radiation-sensitive mutant of a human bladder carcinoma cell line. No difference in the rate or extent of double-strand break rejoining was found using the techniques of neutral filter elution and pulsed-field gel electrophoresis. In contrast, significant differences in repair fidelity, measured by plasmid reconstitution, were found. The parent line had a repair fidelity of 84.7% compared with 58.9% for S40b (P = 0.0003). It is suggested that repair fidelity can be an important determinant of radiosensitivity in human tumour cells.

Carcinoma↗
PubMed2026

Perioperative Depression and Anxiety Care in Older Patients: A Randomized Clinical Trial.

IMPORTANCE: Depression and anxiety are common among older adults undergoing surgery and are associated with adverse postoperative outcomes. However, effective tailored perioperative mental health interventions are lacking. OBJECTIVE: To evaluate a perioperative intervention to optimize mental health. DESIGN, SETTING, AND PARTICIPANTS: A single-blind, hybrid, type 1, effectiveness-implementation randomized clinical trial was conducted (November 1, 2022, to March 31, 2025), with 3-month postoperative follow-up, at a US academic and community practice hospital network. Participants were 60 years or older; scheduled for cardiac, oncologic, or orthopedic surgery; and had clinically meaningful symptoms of depression and/or anxiety based on the Patient Health Questionnaire-Anxiety and Depressive Symptom (PHQ-ADS) scale. A total of 3159 patients were screened for eligibility, with 1518 ineligible, 1079 declining participation, and 236 excluded for other reasons. A total of 326 patients were enrolled and randomized (1:1), with 20 excluded after surgery cancelation. INTERVENTION: Participants were assigned to receive a perioperative intervention combining psychological management and pharmacologic optimization or enhanced usual care (materials for self-managing symptoms). MAIN OUTCOMES AND MEASURES: The primary outcome was change in PHQ-ADS score from baseline to 3 months after surgery. Other outcomes included persistent postsurgical pain, delirium, falls, quality of life, patient satisfaction, length of stay, and rehospitalizations. Implementability was evaluated through semistructured interviews and reach, acceptability, feasibility, appropriateness, and fidelity measures. RESULTS: A total of 306 older adults were included in analysis (mean [SD] age, 68.5 [6.1] years; 209 [68.3%] female; 153 randomized to intervention and 153 randomized to enhanced usual care): 102 cardiac, 100 oncologic, and 104 orthopedic patients. Participants' mean (SD) baseline PHQ-ADS score was 18.5 (7.4). At 3 months, there was a significant decrease in PHQ-ADS scores in the intervention group compared with the enhanced usual care group (mean difference, 2.20; 95% CI, 0.16-4.24; P = .03). Effects varied by surgical subgroups (oncologic patients: mean difference, 4.93; 95% CI, 1.51-8.36; P = .005; cardiac patients: mean difference, 2.68; 95% CI, -0.98 to 6.35; P = .15; and orthopedic patients: mean difference, -1.11; 95% CI, -4.62 to 2.40; P = .54). Patients and interventionists perceived the intervention as appropriate, with high-fidelity delivery and broad reach across the target population. CONCLUSIONS AND RELEVANCE: In this randomized clinical trial, psychological management and pharmacologic optimization reduced anxiety and depression in older adults undergoing surgery. Future studies should assess reproducibility and determine which patients benefit most. TRIAL REGISTRATION: ClinicalTrials.gov Identifiers: NCT05575128, NCT05685511, and NCT05697835.

Humans↗
PubMed1986

Mutational specificity of animal cell DNA polymerases.

Since DNA polymerases are involved in DNA replication, recombination, and repair, the frequency with which these enzymes commit errors during synthesis is likely to be an important factor in controlling mutation rates in cells. The fidelity of DNA polymerases was originally studied by following misincorporation using synthetic nucleic acid templates containing only one or two bases. Later, by assaying for reversion of an amber codon after copying phi X174 single-stranded DNA molecules, the base substitution accuracy of in vitro DNA synthesis on natural DNA was determined. Most recently, a forward mutation assay has been developed that uses gap-filling synthesis on an M13mp2 DNA template, thus permitting the detection of a variety of different errors during DNA synthesis on natural DNA templates. Detailed mutational spectra for animal cell polymerases-alpha, beta, and gamma have been determined and demonstrate that a variety of errors can be generated by these purified enzymes. The frequencies of base mispairs, base additions, and deletion errors by DNA polymerases vary widely and depend on both the DNA sequence and the enzyme used. An understanding of the mechanisms by which DNA polymerases avoid or generate various mutations depends on the definition of the parameters that influence the frequency and specificity of particular errors. Future experiments will combine the use of the methods available to measure fidelity with advances in DNA replication enzymology and should lead to exciting new insights into the mechanisms of spontaneous mutagenesis.

Animals↗
PubMed1987

Drug resistance and DNA repair.

DNA repair confers resistance to anticancer drugs which kill cells by reacting with DNA. A review of our current information on the topic will be presented here. Our understanding of the molecular biology of repair of 0(6)-alkylguanine adducts in DNA has advanced as a result of the molecular cloning of the E. coli ada gene but the precise role of this lesion in the cytotoxic effects of alkylating agents in mammalian cells is not completely understood. Less progress has been made in understanding the enzymology and molecular biology of DNA cross-link repair even though such lesions are important for the cytotoxic effects of the widely used bifunctional alkylating agents and platinum compounds. It is evident that drug sensitive or resistant phenotypes are as highly complex as are the effects of DNA damage on cell metabolism and various aspects of these effects are discussed. Few clear correlations have been made between quantitative differences in DNA repair capacity and cellular sensitivity but assays which were developed to measure fidelity and intragenomic heterogeneity in DNA repair are beginning to be applied. Such studies may reveal subtle differences between sensitive and resistant cell lines. The molecular cloning of human DNA repair genes by transfection into drug sensitive rodent cells has been attempted. Some success has been achieved in this area but the functions of the cloned genes have yet to be identified.

Animals↗
PubMed1991

Exonucleolytic proofreading of leading and lagging strand DNA replication errors.

We have asked whether exonucleolytic proofreading occurs during simian virus 40 origin-dependent, bidirectional DNA replication in extracts of human HeLa cells. In addition, we have compared the fidelity of leading and lagging strand DNA synthesis. In a fidelity assay that scores single-base substitution errors that revert a TGA codon in the lacZ alpha gene in an M13mp vector, providing an excess of a single dNTP substrate over the other three dNTP substrates in a replication reaction generates defined, strand-specific errors. Fidelity measurements with two vectors having the origin of replication on opposite sides of the opal codon demonstrate that error rates for two different A.dCTP and T.dGTP mispairs increase when deoxyguanosine monophosphate is added to replication reaction mixtures or when the concentration of deoxynucleoside triphosphates is increased. The data suggest that exonucleolytic proofreading occurs on both strands during bidirectional replication. Measurements using the two simian virus 40 origin-containing vectors suggest that base substitution error rates are similar for replication of the leading and lagging strands.

Antigens, Polyomavirus Transforming↗
PubMed1985

DNA polymerase alpha and models for proofreading.

Using a modified system to measure fidelity at an amber site in phi X174, we have employed DNA polymerase alpha to test different mechanisms for proofreading. DNA polymerase alpha does not exhibit the characteristics of "kinetic proofreading" seen with procaryotic polymerases. Polymerase alpha shows no evidence for a "next nucleotide" effect, and added deoxynucleoside monophosphates do not alter fidelity. Pyrophosphate, which increases error rates with a procaryotic polymerase, appears to weakly improve polymerase alpha fidelity. DNA polymerase alpha does exhibit a dramatic increase in error rate in the presence of a deoxycytidine thiotriphosphate (dCTP alpha S), but this enhanced mutagenesis also occurs under conditions where kinetic proofreading should be otherwise defeated. This particular effect with dCTP alpha S appears specific for DNA polymerase alpha and is not seen with the other polymerases tested.

Animals↗
PubMed1977

Physiologic determinants of left ventricular strength-interval curve of the dog.

Strength-interval curves, relating an index of the contractile vigor of premature beats to their coupling intervals, were elicited in anesthetized, open-chest dogs prepared for atrial or ventricular pacing and the high-fidelity measurement of left ventricular pressure. During inotropic interventions, changes of the curves were evaluated in terms of the parameters (slopes and intercepts) of their straight lines of best fit. These parameters were altered by isoproterenol, propranolol, and heart rate, and were correlated closely with paired values of isovolumic Vmax (of driven beats). The strength-interval curves were reproducible and were not affected by large changes of venous return or arterial blood pressure. These results provide a basis for the use of strength-interval curves for the evaluation of ventricular contractile state, using fluid-filled catheters for the measurement of left ventricular pressure.

Animals↗
PubMed1976

Ventricular pressure-volume curve indices change with end-diastolic pressure.

Many indices have been proposed to describee the diastolic pressure-volume curve mathematically and permit quantification of the elastic properties of the myocardium itself in hopes that changes in the muscle caused by disease would b.e reflected in the diastolic pressure-volume curve. To date, none of the proposed indices has been shown convincingly to discriminate one group of patients from another. While this situation in part arises from the relatively large amount of noise introduced by the technical difficulties of measuring synchronous pressures and volumes during diastole in man, ther is a more fundamental difficulty. In practice, one can measure only a short segment of the entire pressure-volume curve, and the values of all diastolic pressure-volume curve parameters investigated change significantly when one uses different segments of the same pressure-volume curve to compute them. These results were derived from relatively noise-free pressure-volume curves obtained by filling nine excised dog left ventricles at a known rate and monitoring pressure-volume curve used to compute the parameter. Merely increasing measurement fidelity will not resolve this problem, because none of these parameters accurately characterizes the entire diastolic pressure-volume curbe from a segment like that which one can reasonably expect to obtain from humans.

Animals↗
PubMed1990

DNA polymerase alpha from HeLa cells synthesizes DNA with high fidelity in a reconstituted replication system.

To determine the contribution that DNA polymerase alpha makes to the overall DNA replication fidelity in mammalian systems, we measured the fidelity of replication of the SV40-based shuttle vector, pZ189, in a reconstituted in vitro DNA replication system which contained purified HeLa DNA polymerase alpha (in addition to single-stranded DNA binding protein, topoisomerase II, DNA ligase, 5'----3' exonuclease, ribonuclease H, and SV40 T-antigen). We found that DNA polymerase alpha is highly accurate when carrying out bidirectional replication in this system. This high fidelity of replication by DNA polymerase alpha in the reconstituted replication system contrasts with a relatively low fidelity of gap-filling DNA synthesis on the same target gene by purified HeLa cell DNA polymerase alpha in the absence of other replication factors. The fidelity of DNA replication by DNA polymerase alpha, although relatively high in the reconstituted system, is about 4-fold lower than DNA replication in a crude HeLa cell extract which contains additional replication factors including DNA polymerase delta. These results demonstrate that DNA polymerase alpha has the capacity to replicate DNA with high fidelity when carrying out semiconservative DNA replication in a minimal reconstituted replication system, but additional cellular factors not present in the reconstituted system may contribute to the higher replication fidelity of the crude system.

Cell-Free System↗
PubMed1987

Echocardiographic left ventricular mass and function in the hypertensive baboon.

Nonhuman primates with chronic systemic hypertension provide an ideal model for studying structural and functional alterations associated with compensatory cardiac hypertrophy. Since noninvasive techniques are useful for the longitudinal evaluation of these animals, we sought to critically asses the M-mode echocardiographic estimation of left ventricular mass in the baboon and to characterize estimates of left ventricular size and function in baboons with chronic renal hypertension. In 23 baboons (12 normotensive, 11 chronic hypertensive), M-mode echocardiography-determined left ventricular mass was 73 +/- 13 (SE) g as compared with the necropsy weight of 69 +/- 11 g (p = NS), and the correlation was excellent (r = 0.94). When 30 chronically hypertensive baboons being observed longitudinally were compared with 10 normotensive control animals studied under identical conditions, several differences were noted in measures derived from echocardiography and high fidelity pressure measurements. Left ventricular systolic pressure was considerably higher in the hypertensive baboons (113 +/- 23 vs 90 +/- 11 mm Hg; p less than 0.001), as was left ventricular mass (148 +/- 60 vs 103 +/- 38 g; p less than 0.03). However, since the ratio of posterior wall thickness to cavity dimension was larger in the hypertensive baboons (0.52 +/- 0.17 vs 0.43 +/- 0.07; p less than 0.05), this concentric hypertrophy maintained values for left ventricular meridional stress at the same level as in the control animals. Despite matched heart rate and left ventricular stress, the rates of change in left ventricular dimensions and wall thickness in systole and diastole were all approximately 25% less in the hypertrophied baboons.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1988

Fidelity of a human cell DNA replication complex.

We have measured the fidelity of bidirectional, semiconservative DNA synthesis by a human DNA replication complex in vitro. Replication was performed by extracts of HeLa cells in the presence of simian virus 40 (SV40) large tumor antigen by using a double-stranded phage M13mp2 DNA template containing the SV40 origin of replication and either of two different target sequences for scoring mutations in the lacZ alpha-complementation gene, which encodes the alpha region (specifying the amino-terminal portion) of beta-galactosidase. Replicative synthesis was substantially more accurate than synthesis by the human DNA polymerase alpha-DNA primase complex purified from HeLa cell extracts by immunoaffinity chromatography, suggesting that additional factors or activities in the extract may increase fidelity during bidirectional replication. However, by using a sensitive opal codon reversion assay, single-base substitution errors were readily detected in the replication products at frequencies significantly higher than estimated spontaneous mutation rates in vivo. These data suggest that additional fidelity factors may be present during chromosomal replication in vivo and/or that the fidelity of replication alone does not account for the low spontaneous mutation rates in eukaryotes.

Antigens, Polyomavirus Transforming↗
PubMed1977

Infidelity of DNA synthesis as related to mutagenesis and carcinogenesis.

An assay system has been developed for measuring the fidelity of DNA synthesis in vitro by using synthetic polynucleotide templates and purified DNA polymerases. Nearest-neighbor analysis of the synthesized product indicates that noncomplementary nucleotides are incorporated as single base substitutions. The accuracy of DNA synthesis can be decreased by (1) prior alkylation of the template, (2) increasing the relative concentration of incorrect nucleotides, and (3) addition of specific metal salts to the reaction mixture. As an initial evaluation of the utility of this system, the effects of 31 metal salts on the fidelity of DNA synthesis have been determined. The results indicate that potential metal mutagens and/or carcinogens may be detected by measuring alterations in the fidelity of DNA synthesis.

Avian Myeloblastosis Virus↗
PubMed1977

Turbulence measurement by the pulse luminescence method using a nitrogen pulse laser.

In order to visualize and measure with ease the velocity distribution and diffusion of turbulent flow, the pulse luminescence method was investigated. Turbulence intensity was obtained from the turbulent diffusion patterns by Taylor's diffusion theory. Apparatus was developed for easier measurement. A nitrogen pulse laser was used for instantaneous, high-power excitation. With the use of a night vision scope a bright image was recorded by a TV camera and video tape recorder. The optimum concentration of LC-G1A luminescent particles was about 0-05% wt for the measurement. High fidelity of the particles as an indicator of the fluid velocity was confirmed. It was demonstrated that the turbulence intensity could be visualized and measured quantitatively by the pulse luminescence method.

Lasers↗