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D C Thomas

Publications and source records attributed to D C Thomas.

At least 109 records · Page 6Linked to original sources

Fidelity of animal cell DNA polymerases alpha and delta and of a human DNA replication complex.

We are investigating the mechanisms by which mutations are produced or avoided during DNA synthesis. Using in vitro fidelity assays, we have defined the error frequency and mutational specificity of the replicative animal cell DNA polymerases (alpha and delta). With DNA polymerase alpha or the four-subunit DNA polymerase alpha-DNA primase complex, neither of which contains detectable associated exonuclease activity, the fidelity of the polymerization step is low relative to spontaneous mutation rates in vivo. DNA polymerase delta is much more accurate, partly due to proofreading by the 3'----5' exonuclease activity associated with this polymerase. These fidelity studies have been extended to the replication apparatus present in extracts of human HeLa cells. The replication complex is highly accurate, suggesting that additional fidelity components are operating in the extract during bidirectional, semiconservative replication of double-stranded DNA. Nevertheless, in highly sensitive reversion assays, base substitution errors can be readily detected at frequencies greater than the estimated rate of spontaneous mutation in vivo. This suggests that fidelity components may be missing and/or that human cells depend heavily on postreplicative repair processes to correct replication errors.

Animals↗

Nested case-control and case-cohort methods of sampling from a cohort: a critical comparison.

The recently developed case-cohort method of sampling from a cohort is compared with the nested case-control method. Corrected asymptotic relative efficiency results show that the case-cohort design for single "disease" outcomes offers less improvement for intervention trials for which there is no random censoring than originally suggested. Furthermore, simulation results indicate that if there is moderate random censoring or staggered entry, the case-cohort method can do substantially worse than the nested case-control method.

Case-Control Studies↗

A model for dose rate and duration of exposure effects in radiation carcinogenesis.

Multistage models have been used to describe various features of the incidence of cancer including the shape of the age-incidence curve; the influence of age at, duration of, and time since exposure; and the synergistic effect of exposure to multiple carcinogens. However, the models require from five to seven distinct transformations that must occur in a particular sequence. The lack of experimental support for so many events suggests a simpler model involving only two mutational events with a proliferative advantage for intermediate-stage cells. Neither model easily explains the paradoxical phenomenon that protraction of low linear energy transfer (LET) radiation leads to lower risks per unit of total exposure, whereas the reverse occurs for high-LET radiation. In this paper, a three-stage model is considered that consists of two mutations at homologous sites, either or both of which might be induced by radiation, followed by activation of the transformed oncogene, which is not induced by radiation. Single-stranded lesions are potentially repairable, whereas double-stranded lesions may increase the proliferation rate. For low-LET radiation, these two mutations are more likely to occur as the result of independent transversals of a cell by separate quanta of radiation, whereas for high-LET radiation, they are more likely to occur simultaneously as the result of a single particle. The predictions of the model are illustrated for various patterns of exposure and choices of model parameters. Various tests of the proposed model are discussed.

Animals↗

Survival models for familial aggregation of cancer.

It has recently been shown that the relative risks of the order of 2 to 4 that are frequently found for cancer among relatives of affected cases are unlikely to be explainable by shared environmental risk factors. Classical methods of epidemiological analysis are not well suited to such analysis because they assume that the outcomes of each individual are independent. Classical methods of genetic analysis, on the other hand, are limited in their handling of environmental factors and variable ages of onset. The recent development of random effects models for survival analysis, however, appears to bridge this gap. Specifically, a proportional hazards model is postulated for the effects of measured covariates and of one or more components of frailty that are unmeasured but assumed to have some common distribution and known covariance structure within each family. From these assumptions, the posterior expectation of the hazard for each individual can be derived, given the covariate value and the observed and expected disease history of the family. These are then treated as known in a standard partial likelihood analysis; this is essentially a form of expectation-maximization algorithm. However, this does not provide a valid estimate of the covariance matrix because it fails to take account of the variability in the estimates of the frailties; an alternative approach using the imputation-posterior algorithm is suggested. This paper describes extensions of this approach to multivariate frailty distributions, modifications for application to pedigree and case-control studies, some simulation results, and applications to studies of breast cancer in twins and of lung cancer in relation to family smoking habits.

Adenocarcinoma↗

Preferential DNA repair of (6-4) photoproducts in the dihydrofolate reductase gene of Chinese hamster ovary cells.

We have developed a method to quantify (6-4) photoproducts in genes and other specific sequences within the genome. This approach utilizes the following two enzymes from Escherichia coli: ABC excinuclease, a versatile DNA repair enzyme which recognizes many types of lesions in DNA, and DNA photolyase, which reverts pyrimidine dimers. DNA is isolated from UV irradiated Chinese hamster ovary cells and digested with a restriction enzyme. Pyrimidine dimers, the major photoproduct produced at biological UV fluences, are then completely repaired by treatment with DNA photolyase. The photoreactivated DNA is treated with ABC excinuclease, electrophoresed in an alkaline agarose gel, transferred to a support membrane and probed for specific genomic sequences. Net incisions produced by ABC excinuclease following photoreactivation are largely due to the presence of (6-4) photoproducts. These adducts are quantitated by measuring the reduction of intensity of the full length fragments on the autoradiogram. Using this approach we have shown that (6-4) photoproducts are produced at equal frequency in the dihydrofolate reductase coding sequence and in its 3'-flanking, noncoding sequences and that the formation of (6-4) photoproducts is linear in both sequences up to a UV dose of 60 J/m2. The repair of (6-4) photoproducts in these DNA sequences was measured after a dose of 40 J/m2 over 4-, 8-, and 24-h time periods. The (6-4) photoproducts are repaired more efficiently than pyrimidine dimers in both sequences and there is preferential repair of (6-4) photoproducts in the dihydrofolate reductase gene compared with the downstream, noncoding sequences.

Animals↗

Tropism and histopathology of the D, B, K, and MM variants of encephalomyocarditis virus.

Variants of encephalomyocarditis virus (EMCV), which are immunologically indistinguishable by hyperimmune serum, produce different disease syndromes in mice. For instance, in ICR Swiss male mice, EMCV-B produces no overt illness, EMCV-MM produces severe neurological signs followed by death, EMCV-D destroys pancreatic beta cells producing a disease syndrome resembling insulin-dependent diabetes mellitus, and EMCV-K is lethal but produces no overt signs of infection. The present study was done to determine the tissue tropism and histopathology of each of these EMCV variants in the ICR Swiss mouse model. The data show the highest concentrations in the following organs: EMCV-D in the pancreas, EMCV-B in the pancreas, EMCV-MM in the cerebrum, and EMCV-K in the medulla/brainstem. They also show that the pathological lesions produced by each variant correlate well with viral titers.

Animals↗

Diagnostic radiography as a risk factor for chronic myeloid and monocytic leukaemia (CML).

This interview study included 136 Los Angeles County residents aged 20-69 with CML diagnosed from 1979 to 1985 (cases) and 136 neighbourhood controls. During the 3-20 years before diagnosis of the case, more cases than controls had radiographic examinations of the back, gastrointestinal (GI) tract and kidneys, and cases more often had GI and back radiography on multiple occasions (odds ratio (OR) for back X-rays on five or more occasions = 12.0; P less than 0.01). Published estimates were used to assign a minimum dose to the active bone marrow for various radiographic procedures. ORs were estimated for cumulative marrow doses for each of four time periods (3-5 years, 6-10 years, 11-20 years and 3-20 years before the diagnosis of the case). The ORs for exposure to 0.99, 100-999, 1000-1999 and greater than or equal to 2000 mrad in the 3-20 years before diagnosis were 1.0, 1.4, 1.6 and 2.4 (P for highest exposure category and P for trend both less than 0.05). The association was strongest for the period 6-10 years before diagnosis, and the effects of radiation exposure during this period remained significant after consideration of other risk factors in a logistic regression analysis.

Adult↗

Noise trauma in the aetiology of acoustic neuromas in men in Los Angeles County, 1978-1985.

The aim of this study was to investigate whether occupational and other suggested brain tumour risk factors relate to the development of acoustic neuromas (AN) in men. Responses to interviews were compared for 86 AN patients and 86 neighbourhood controls. During the period 10 or more years before the year of diagnosis of the case, more cases than controls had a job involving exposure to extremely loud noise; noise exposure was determined by a blinded review of job histories and linkage to the National Occupational Hazards Survey data base (odds ratio (OR) = 2.2, 95% confidence interval (CI) = 1.12, 4.67). A dose-response analysis showed an increase in risk related to number of years of job exposure to extremely loud noise (P for trend = 0.02) with an OR of 13.2 (CI = 2.01, 86.98) for exposure for 20 or more years during the period up to 10 years before diagnosis. We propose that the findings in this study which identify noise as a risk factor support the hypothesis that mechanical trauma may contribute to tumorigenesis.

Adult↗

The role of interferon in the protection of ICR Swiss male mice by the nondiabetogenic variant of encephalomyocarditis virus against virus-induced diabetes mellitus.

The production of murine diabetes mellitus by the diabetogenic variant of encephalomyocarditis virus (EMCV-D) is prevented in mice preinfected for 24 h with nondiabetogenic virus (EMCV-B). It has been suggested that the protection of the animals is due to the induction of interferon (IFN) by EMCV-B. The present study was done to investigate further the role of IFN in the protection of male ICR Swiss mice against the diabetogenic effects of EMCV-D virus. The results show that this mouse strain is protected only by viable EMCV-B given by either the i.v. or i.p. route of inoculation and that the protection is not abrogated by anti-IFN gamma-globulin. Further, the animals were not protected by either IFN-alpha, IFN- beta, or IFN- alpha/beta at concentrations shown previously to protect mice against the lethal effects of other variants of EMCV. The data provide further evidence that, in the ICR Swiss mouse, IFN does not play a major role in protecting pancreatic beta-cells against infection by EMCV-D.

Animals↗

Analysis of fidelity mechanisms with eukaryotic DNA replication and repair proteins.

We are investigating the mechanisms for producing or avoiding errors during DNA synthesis catalyzed by DNA replication and repair proteins purified from eukaryotic sources. Using assays that monitor the fidelity of a single round of DNA synthesis in vitro, we have defined the error frequency and mutational specificity of the four classes of animal cell DNA polymerases (alpha, beta, delta, gamma), and the fidelity of an SV40 origin-dependent DNA replication complex in extracts of HeLa cells.

Animals↗

Differing attachment of diabetogenic and nondiabetogenic variants of encephalomyocarditis virus to beta-cells.

The D variant of encephalomyocarditis (EMC-D) virus does not induce the production of interferon (IFN) and produces an insulin-dependent diabetes mellitus (IDDM)-like syndrome in certain mouse strains. In contrast, the B variant (EMC-B) virus, which is serologically identical to EMC-D virus, is a good inducer of IFN and is nondiabetogenic. It has been postulated that IFN may play a major role in determining the ability of these two viruses to infect pancreatic beta-cells. However, recent studies have shown that ICR Swiss and BALB/cByJ male mice are not protected by IFN against EMC-D virus-induced IDDM. Furthermore, treatment of these two strains of mice with anti-IFN gamma-globulin before infection with EMC-B virus does not result in diabetes. These observations suggest that mechanisms other than the IFN system are involved in determining the ability of the viruses to infect and destroy beta-cells. Studies were initiated to identify other mechanisms of action. In this communication, we show that up to six times more EMC-D than EMC-B virus attaches to primary beta-cells extracted from male ICR Swiss mice. This difference in ability to attach to beta-cells may account for the difference in the diabetic potential of this mouse strain.

Adsorption↗

Surface stereophotogrammetry of thoracic kyphosis.

The thoracic kyphosis angles of 16 normal individuals, 10 patients with Scheuermann's disease and 11 with adolescent idiopathic scoliosis were measured both radiographically and from Integrated Shape Imaging System (ISIS) scans obtained by surface stereophotogrammetry. There was a high correlation between the two measures. The method of kyphosis measurement from ISIS scans was then used for 30 patients with adolescent idiopathic scoliosis who underwent corrective surgery. A significant reduction in thoracic kyphosis was observed postoperatively. In another group of 28 patients managed conservatively by bracing, some hypokyphosis developed after treatment. However, we found no association between hypokyphosis and curve progression.

Adolescent↗

Doppler ultrasound in the nonpregnant pelvis.

The reproducibility of Doppler ultrasound waveforms within gynecology has not been previously assessed. A study was conducted of Doppler ultrasound signals from the uterine and ovarian arteries in nonpregnant women. The aim of the study was to compare the results of two different observers and also to determine the influence of a time delay (30 minutes later). A second aim was to observe the influence of the menstrual cycle on Doppler ultrasound signals. Pulsatility indices were calculated for each series of Doppler signals. The results show that the technique has a large interobserver difference and its use in the deep pelvic vessels for research purposes is of doubtful value at present.

Adult↗

Personal and family history of lung disease as risk factors for adenocarcinoma of the lung.

To identify risk factors for adenocarcinoma of the lung, a population-based case-control study of 336 female cancers of this cell type and an equal number of neighborhood controls was conducted between 1983 and 1986. After adjusting for personal smoking, personal and family histories of lung disease emerged as additional risk factors. A personal history of any lung disease was associated with a 40% increase in risk [smoking adjusted relative risk (SARR) = 1.4, 95% confidence interval (CI) = 1.0, 2.0] with a more marked increase in risk for lung diseases occurring during childhood (SARR = 1.9, 95% CI = 1.2, 3.2) and for tuberculosis (SARR = 10.0, 95% CI = 1.1, 90.1). Family histories of tuberculosis (SARR = 2.0, 95% CI = 1.1, 3.6) and of lung cancer (SARR = 3.9, 95% CI = 2.0, 7.6) were also risk factors for adenocarcinoma of the lung. Increasing risk was observed with decreasing intake of dietary beta-carotene. After adjusting for personal smoking, women in the lowest quartile of intake showed a two-fold increased risk relative to those in the highest quartile of intake (P = 0.003). There were also some suggestive differences between cases and controls in their reproductive history and hormone use.

Adenocarcinoma↗

Prior exposure to medical and dental x-rays related to tumors of the parotid gland.

Findings from this population-based study in Los Angeles County suggest, for the first time, that tumors of the parotid gland are related to prior exposure to diagnostic medical and dental radiography. Responses to interviews with 408 patients with a parotid tumor (269 benign tumors and 139 malignant tumors) were compared to responses of 408 neighborhood controls. Cumulative exposure of the parotid gland from diagnostic radiography was associated with a dose-related increase in risk of malignant tumors (P for trend less than .05; relative risk for exposure to greater than or equal to 50 rad = 3.4; 95% confidence interval = 1.02-11.46). Benign tumors showed a weaker positive association, and exposure before age 20 to a major diagnostic examination (full-mouth or panoramic dental radiography or medical radiography to the head) increased risk (relative risk = 1.8; confidence interval = 1.13-2.91). This study also confirmed the association of malignant tumors with prior radiation treatment to the head or neck; 28% of these tumors are attributable to exposure of the parotid gland from diagnostic and therapeutic radiation.

Adult↗

Purification and enzymological characterization of DNA-dependent ATPase IV from the Novikoff hepatoma.

DNA-dependent ATPase IV has been purified to near homogeneity from the Novikoff rat hepatoma. The enzyme is devoid of DNA polymerase, RNA polymerase, exonuclease, endonuclease, phosphomonoesterase, 3'- or 5'-phosphodiesterase, polynucleotide kinase, protein kinase, topoisomerase, helicase or DNA reannealing activities at a detection level of 10(-5) to 10(-7) relative to the ATPase activity. The enzyme is a monomer of Mr 110,000, has a sedimentation coefficient of 5.9 S, a Stokes radius of 40 A and a frictional coefficient of 1.32. In the presence of Mg2+ ion and a polynucleotide effector, ATPase IV hydrolyzes either ATP or dATP to the nucleoside diphosphate plus Pi. Other ribo- or deoxyribonucleoside triphosphates are not substrates. ATPase IV utilizes double-stranded DNA and single-stranded DNA as effector; however, it does not utilize poly(dT). The Km for dsDNA or ssDNA is 2.2 microM (nucleotide). A variety of ATP analogues were found to be competitive inhibitors of ATPase IV.

Adenine Nucleotides↗

Methods for testing interactions, with applications to occupational exposures, smoking, and lung cancer.

Various approaches to assessing the interaction between smoking and occupational exposures are described. The definition of interaction depends on the measure of association under consideration and can be expressed in terms of disease risk, time, or dose. Simple descriptive methods and maximum likelihood model fitting methods are presented for analyzing interactions in terms of joint effects on disease risk. Methods for assessing the influence of exposures on times to disease, using appropriate denominators, are also described. The various approaches are illustrated with published data on lung cancer in relation to asbestos, radon daughters, chloromethyl ethers, and arsenic. Some of the mechanisms that can be invoked to explain the observed patterns include initiation and promotion, lung clearance, transport across cell membranes, and mucous secretion.

Arsenic↗

General method for quantifying base adducts in specific mammalian genes.

A general method has been developed to measure the formation and removal of DNA adducts in defined sequences of mammalian genomes. Adducted genomic DNA is digested with an appropriate restriction enzyme, treated with Escherichia coli UvrABC excision nuclease (ABC excinuclease), subjected to alkaline gel electrophoresis, and probed for specific sequences by Southern hybridization. The ABC excinuclease incises DNA containing bulky adducts and thus reduces the intensity of the full-length fragments in Southern hybridization in proportion to the number of adducts present in the probed sequence. This method is similar to that developed by Bohr et al. [Bohr, V. A., Smith, C. A., Okumoto, D. S. & Hanawalt, P. C. (1985) Cell 40, 359-369] for quantifying pyrimidine dimers by using T4 endonuclease V. Because of the wide substrate range of ABC exinuclease, however, our method can be used to quantify a large variety of DNA adducts in specific genomic sequences.

4-Nitroquinoline-1-oxide↗