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D C Thomas

Publications and source records attributed to D C Thomas.

At least 55 records · Page 3Linked to original sources
PubMed1997

Analysis of gene-smoking interaction in lung cancer.

The Louisiana Lung Cancer Dataset, consisting of 337 extended pedigrees, is analyzed to determine whether a major Mendelian gene interacts with cumulative tobacco smoking (pack-years). The proportional hazards model is utilized, as it is a natural framework for estimating relative risks while adjusting for variability in age of disease onset. Segregation analyses show evidence that a Mendelian gene is segregating in these families, with the most parsimonious model, including sex, pack-years, pack-years squared, and a dominant major gene. The estimated frequency of the high-risk allele is 2% and carriers are estimated to have relative risk of 17.3 for developing lung cancer, compared to noncarriers. The addition of a gene x pack-years interaction does not significantly improve the fit of the model, indicating that on a multiplicative scale, these two factors independently influence lung cancer risk. Smoking history is missing for 23% of the study subjects and degree of "missingness" depends on disease status, age, and birth-year. To account for the nonrandomness of the missing data, a Markov chain Monte Carlo method for covariate imputation is proposed and implemented. Results from this analysis also support a nonsignificant gene-smoking interaction and an allele frequency of 2%, but a lower genetic relative risk (9.0) compared to the "complete case" analysis.

Age of Onset↗
PubMed1997

A Bayesian approach to multipoint mapping in nuclear families.

We describe the application of a Markov Chain Monte Carlo approach for multipoint mapping of a quantitative trait locus to the Nuclear Families simulated data. The method involves repeated sampling of genotype vectors for each nuclear family from their conditional distributions, given phenotypes, markers, and model parameters, using peeling and gene dropping, followed by random sampling of each model parameter given genotypes and the other parameters. Reversible jump methods are used to sample the number of trait loci.

Bayes Theorem↗
PubMed1996

Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis.

A two-hybrid system was used to screen yeast and human expression libraries for proteins that interact with mismatch repair proteins. PCNA was recovered from both libraries and shown in the case of yeast to interact with both MLH1 and MSH2. A yeast strain containing a mutation in the PCNA gene had a strongly elevated mutation rate in a dinucleotide repeat, and the rate was not further elevated in a strain also containing a mutation in MLH1. Mismatch repair activity was examined in human cell extracts using an assay that does not require DNA repair synthesis. Activity was inhibited by p21WAF1 or a p21 peptide, both of which bind to PCNA, and activity was restored to inhibited reactions by addition of PCNA. The data suggest a PCNA requirement in mismatch repair at a step preceding DNA resynthesis. The ability of PCNA to bind to MLH1 and MSH2 may reflect linkage between mismatch repair and replication and may be relevant to the roles of mismatch repair proteins in other DNA transactions.

Adaptor Proteins, Signal Transducing↗
PubMed1996

Simultaneously modelling censored survival data and repeatedly measured covariates: a Gibbs sampling approach.

Recent methodologic developments in the analysis of longitudinal data have typically addressed one of two aspects: (i) the modelling of repeated measurements of a covariate as a function of time or other covariates, or (ii) the modelling of the effect of a covariate on disease risk. In this paper, we address both of these issues in a single analysis by modelling a continuous covariate over time and simultaneously relating the covariate to disease risk. We use the Markov chain Monte Carlo technique of Gibbs sampling to estimate the joint posterior distribution of the unknown parameters of the model. Simulation studies showed that jointly modelling survival and covariate data reduced bias in parameter estimates due to covariate measurement error and informative censoring. We illustrate the methodology by application to a data set that consists of repeated measurements of the immunologic marker CD4 and times of diagnosis of AIDS for a cohort of anti-HIV-1 positive recipients of anti-HIV-1 positive blood transfusions. We assume a linear random effects model with subject-specific intercepts and slopes and normal errors for the true log and square root CD4 counts, and a proportional hazards model for AIDS-free survival time expressed as a function of current true CD4 value. On the square root scale, the joint approach yielded a mean slope for CD4 that was 7 per cent steeper and a log relative risk of AIDS that was 35 per cent larger than those obtained by analysis of the component sub-models separately.

Acquired Immunodeficiency Syndrome↗
PubMed1996

Development and initial testing of a pediatric centrifugal blood pump.

BACKGROUND: We are developing a miniaturized centrifugal blood pump for use as a temporary cardiac assist device in neonatal and pediatric sized patients. This pump has a very low priming volume of 13 mL. A small motor stator has also been designed, which resulted in a device that can be placed very close to the patient, thereby minimizing overall circuit volume. METHODS: Testing to date has included in vitro hemodynamic performance, in vitro hemolysis generation, and in vivo evaluation in 5 lambs weighing 5.5 to 21 kg. Two lambs underwent peripheral cannulation from external jugular vein to carotid artery, whereas 3 others were cannulated from left atrium to carotid artery. RESULTS: In vitro data demonstrated pump capacity spanning 0.3 to 3.0 L/min and very low hemolysis generation at these conditions. In vivo, the pump functioned satisfactorily for periods up to 148 hours, and the bypass appeared to be well tolerated by the animals. Plasma free hemoglobin levels remained less than 25 mg/dL during all animal experiments. All devices were thrombus-free at explantation. CONCLUSIONS: We conclude that this device has merit as an alternative to current oversized systems used for neonatal and pediatric cardiac assistance. In addition, a chronic neonatal lamb model in which to evaluate pediatric circulatory assist devices has been developed successfully.

Animals↗
PubMed1996

Strand specificity of mutagenic bypass replication of DNA containing psoralen monoadducts in a human cell extract.

Psoralens are mutagenic compounds of vegetable origin that are used as photosensitizing agents in the treatment of various skin diseases, blood cell cancer, and autoimmune disorders. To study the mechanism of mutagenicity of psoralens in humans, we examined the efficiency and fidelity of simian virus 40 origin-dependent replication in a human cell extract of M13mp2 DNA randomly treated with the psoralen derivative 4'-hydroxymethyl-4,5',8-trimethyl psoralen plus UVA irradiation. Replication of DNA treated with variable amounts of 4'-hydroxymethyl-4,5',8-trimethyl psoralen and a fixed UVA fluence was inhibited in a concentration-dependent manner. However, covalently closed monomer-length circular replication products were observed. Product analysis by renaturing agarose gel electrophoresis after cross-linking with 250- to 280-nm UV light indicated that approximately 1 of 9 psoralen monoadducts was bypassed during in vitro replication. Introduction of product DNA into Escherichia coli to score replication errors in the lacZalpha reporter gene demonstrated that replication of the damaged DNA was more mutagenic than was replication of undamaged DNA. Sequence analysis of lacZ mutants revealed that damage-dependent replication errors were predominantly T.A-->C.G transitions, transversions at C.G base pairs, and deletions of single A.T base pairs, the last occurring most frequently in homopolymeric runs. A comparison of error specificities with two substrates having the replication origin asymmetrically placed on opposite sides of the mutational target suggests that the lagging-strand replication apparatus is less accurate than the leading-strand replication apparatus for psoralen monoadduct-dependent deletion errors. A model is proposed based on the preferential loopout of the monoadducted base from the strand that templates retrograde discontinuous synthesis.

Bacteriophage M13↗
PubMed1995

Frequency and fidelity of translesion synthesis of site-specific N-2-acetylaminofluorene adducts during DNA replication in a human cell extract.

We have previously analyzed the effects of site-specific N-2-acetylaminofluorene (AAF) adducts on the efficiency and frameshift fidelity of SV40-based DNA replication in a human cell extract (Thomas, D. C., Veaute, X., Kunkel, T. A., and Fuchs, R. P. P. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 7752-7756). Here we use two sets of substrates to examine the probability of replication termination and error-free and error-prone bypass of AAF adducts. The substrates contained site-specific adducts at one of three guanines in a NarI sequence (5'-GGCGCC-3') placed within the lacZ alpha reporter gene and located on the template for either leading or lagging strand replication. The presence of the adduct at any position strongly reduces the efficiency of a single round of replication in a HeLa cell extract. Product analysis reveals preferential replication of the undamaged strand and termination of replication of the damaged strand occurring one nucleotide before incorporation opposite either a leading or lagging strand adduct. Products resistant to restriction endonuclease cleavage at the adducted site were generated in amounts consistent with 16-48% lesion bypass during replication. Most of this bypass was error-free. However, two-nucleotide deletion errors were detected in the replication products of DNA containing an AAF adduct in either the leading or lagging strand, but only when present at the third guanine position. Collectively, the data suggest that the replication apparatus in a HeLa cell extract generates a template-primer slippage error at an AAF adduct once for every 30-100 bypass events.

2-Acetylaminofluorene↗
PubMed1995

Hypothesis: the risk of childhood leukemia is related to combinations of power-frequency and static magnetic fields.

We present a hypothesis that the risk of childhood leukemia is related to exposure to specific combinations of static and extremely-low-frequency (ELF) magnetic fields. Laboratory data from calcium efflux and diatom mobility experiments were used with the gyromagnetic equation to predict combinations of 60 Hz and static magnetic fields hypothesized to enhance leukemia risk. The laboratory data predicted 19 bands of the static field magnitude with a bandwidth of 9.1 microT that, together with 60 Hz magnetic fields, are expected to have biological activity. We then assessed the association between this exposure metric and childhood leukemia using data from a case-control study in Los Angeles County. ELF and static magnetic fields were measured in the bedrooms of 124 cases determined from a tumor registry and 99 controls drawn from friends and random digit dialing. Among these subjects, 26 cases and 20 controls were exposed to static magnetic fields lying in the predicted bands of biological activity centered at 38.0 microT and 50.6 microT. Although no association was found for childhood leukemia in relation to measured ELF or static magnetic fields alone, an increasing trend of leukemia risk with measured ELF fields was found for subjects within these static field bands (P for trend = 0.041). The odds ratio (OR) was 3.3 [95% confidence interval (CI) = 0.4-30.5] for subjects exposed to static fields within the derived bands and to ELF magnetic field above 0.30 microT (compared to subjects exposed to static fields outside the bands and ELF magnetic fields below 0.07 microT). When the 60 Hz magnetic fields were assessed according to the Wertheimer-Leeper code for wiring configurations, leukemia risks were again greater with the hypothesized exposure conditions (OR = 9.2 for very high current configurations within the static field bands; 95% CI = 1.3-64.6). Although the risk estimates are based on limited magnetic field measurements for a small number of subjects, these findings suggest that the risk of childhood leukemia may be related to the combined effects of the static and ELF magnetic fields. Further tests of the hypothesis are proposed.

Calcium↗
PubMed1995

Genetic epidemiologic analysis of quantitative phenotypes using Gibbs sampling.

We analyzed two quantitative traits (Q1 and Q2) provided in the 'Common Disease' data set with the aim of detecting both genetic and environmental determinants. We used linear regression for screening measured variables, maximum likelihood segregation and linkage analyses for detecting and localizing unmeasured genes, and Gibbs sampling for joint segregation and linkage analyses with estimation of gene-environment interaction and polygenic effects. For both Q1 and Q2, we successfully detected the unmeasured codominant major gene (MG) that was tightly linked to candidate gene C2. We also detected all of the measured variables used in generating Q1 (age, Q3, candidate gene C5) and Q2 (EF). Although our final models differed slightly from the true data generation models, our multifaceted analytic approach was successful in characterizing the determinants of Q1 and Q2.

Alleles↗
PubMed1995

The Utah Leukemia Case-Control Study: dosimetry methodology and results.

This paper discusses the dosimetry methodology used to estimate bone marrow dose and the results of dosimetry calculations for 6,507 subjects in an epidemiologic case-control study of leukemia among Utah residents. The estimated doses were used to determine if a higher incidence of leukemia among residents of Utah could have been attributed to exposure to radioactive fallout from above-ground nuclear weapons tests conducted at the Nevada Test Site. The objective of the dosimetry methodology was to estimate absorbed dose to active marrow specific to each case and each control subject. Data on the residence of each subject were available from records of the Church of Jesus Christ of Latter-day Saints. Deposition of fallout was determined from databases developed using historical measurements and exposure for each subject from each test was estimated using those data. Exposure was converted to dose by applying an age-dependent dose conversion factor and a factor for shielding. The median dose for all case and control subjects was 3.2 mGy. The maximum estimated mean dose for any case or control was 29 +/- 5.6 mGy (a resident of Washington County, UT). Uncertainties were estimated for each estimated dose. The results of the dosimetry calculations were applied in an epidemiological analysis.

Adolescent↗
PubMed1995

The Utah Thyroid Cohort Study: analysis of the dosimetry results.

Above ground testing of nuclear weapons at the Nevada Test Site (NTS) during the 1950s created radioactive fallout that was dispersed into the atmosphere and deposited over a large geographical area of the U.S. One area believed to have received a considerable amount of exposure to radioiodines (131I and 133I) in the fallout was southwest Utah and southeast Nevada. This paper describes the estimates of doses to the thyroid for a cohort of 3,545 subjects who were children during the atmospheric testing period. This group of children was examined for thyroid disease during 1965-1970 and again in 1985-1986. The cohort was made up of children who lived in three counties in 1965: Washington County, Utah; Lincoln County, Nevada; and Graham County, Arizona (originally thought to be an unexposed group). Pathway analysis was used in the dosimetry, considering exposures through the ingestion of milk and vegetables, inhalation of iodine during the passage of the fallout cloud, and external exposure. Specific data were obtained on diet (including sources and levels of milk and vegetables consumed, residence history, and lifestyle) by interviewing the parents or nearest living relative of subjects. The final dosimetry file for each member of the cohort contained specific doses to the thyroid glands and uncertainties (reported as geometric standard deviations, GSD) related to each dose estimate. The mean absorbed dose to the thyroid for subjects living in Washington County, Utah, was 170 mGy; for Lincoln County, Nevada, 50 mGy; and for those living in Graham County, Arizona, 13 mGy. The maximum dose to any subject was 4,610 mGy. There were 10 subjects who had doses greater than 1 Gy. The majority of uncertainty values calculated in this study were GSD values between 2.0 and 4.0. The results of the dosimetry were combined with the results of clinical examinations of the cohort to determine if a causal relationship exists between dose to thyroid from NTS generated radioactive iodines and the incidence of thyroid disease.

Adult↗
PubMed1994

Mutagenic replication in human cell extracts of DNA containing site-specific N-2-acetylaminofluorene adducts.

We have analyzed the effects of site-specific N-2-acetylaminofluorene (AAF) adducts on the efficiency and frameshift fidelity of bidirectional replication of double-stranded DNA in a human cell extract. Plasmid vectors were constructed containing the simian virus 40 origin of replication and single AAF adducts at one of three guanines in the Nar I sequence GGCGCC in a lacZ reporter gene. The presence of an AAF adduct diminishes replication efficiency in HeLa cell extracts by 70-80%. Replication product analyses reveal unique termination sites with each damaged vector, suggesting that when the replication fork encounters an AAF adduct, it often stops before incorporation opposite the adduct. We also observed a higher proportion of products representing replication of the undamaged strand compared to the damaged strand. This suggests that the undamaged strand is replicated more readily, either by uncoupling the first fork to encounter the lesion or by replication using the fork arriving from the other direction. Also included among replication products are covalently closed monomer-length molecules resistant to cleavage at the AAF-modified Nar I site. This resistance is characteristic of substrates containing the AAF adduct, suggesting that translesion bypass had occurred. Transformation of Escherichia coli cells with the replicated damaged DNA yielded lacZ alpha revertant frequencies significantly above values obtained with undamaged DNA or with damaged DNA not replicated in vitro. This increase was only seen with the substrate modified at the third guanine position. Analysis of mutant DNA demonstrated the loss of a GC dinucleotide at the Nar I sequence. Generation of this position-dependent AAF-induced frameshift error in a human replication system is consistent with previous observations in E. coli suggesting that, after incorporation of dCMP opposite modified guanine in the third position, realignment of the template-primer occurs to form an intermediate with two unpaired nucleotides in the template strand.

2-Acetylaminofluorene↗
PubMed1994

The basolateral targeting signal in the cytoplasmic domain of glycoprotein G from vesicular stomatitis virus resembles a variety of intracellular targeting motifs related by primary sequence but having diverse targeting activities.

Using systematic site-directed mutagenesis, the basolateral targeting signal in the cytoplasmic domain of glycoprotein G from vesicular stomatitis virus (VSV G) has been localized to an 11-amino acid sequence, which contains two essential residues and a third that makes a minor contribution. A tyrosine at position 19 of the 29-residue carboxyl-terminal cytoplasmic tail is the most important residue and cannot be replaced by other aromatic amino acids, while an isoleucine at position 22, 3 residues carboxyl-terminal to this tyrosine, is also critical but can be replaced by other aliphatic residues. Additionally, an arginine at position 16 makes a minor contribution. Therefore the crucial elements of this targeting signal can be represented by the sequence Y-X-X-aliphatic. While earlier investigation has suggested similarity between basolateral targeting and internalization signals, alignment of this sequence with other cytoplasmic targeting signals suggests the existence of a broad class of homologous targeting motifs that direct protein delivery to a variety of cellular locations. This in turn suggests the existence of a family of homologous receptors, distributed throughout the cell, which differ in their affinity for subsets of these targeting sequences.

Amino Acid Sequence↗
PubMed1994

Defective mismatch repair in extracts of colorectal and endometrial cancer cell lines exhibiting microsatellite instability.

A replication error (RER+) phenotype, characterized by somatic instability in simple repeated sequences, is associated with several types of cancer. To determine if a defect in DNA replication fidelity or repair of replication errors might explain this instability, we compared both processes in cell-free extracts from RER+ endometrial and colorectal cancer cell lines to RER- cell lines. SV40 origin-dependent replication of a microsatellite sequence is highly accurate in cell extracts regardless of their RER phenotype. However, extracts from RER+ cell lines are defective in mismatch repair, while extracts of RER- cell lines are not. Lack of repair was observed when the signal (a nick) for strand-specific repair was either 3' or 5' to the mispair. One colorectal cancer cell line contained deletions in both alleles of the putative mismatch repair gene hMSH2, and one endometrial cancer cell line contained a 4-base pair duplication in one hMSH2 allele. No hMSH2 mutation was detected in the other allele or in the other five RER+ cell lines. Repair was readily detected when each of the defective extracts was mixed with a repair-proficient extract, demonstrating that no trans-acting inhibitor is present. Attempts to complement the repair deficiencies by mixing two different defective extracts identified three combinations that restored repair. The data suggest that: (i) defective repair is associated with colorectal and endometrial cancer and, by extrapolation, with other types of cancer; (ii) mutations in the hMSH2 gene, and possibly other genes, result in defective mismatch repair; (iii) the defect(s) in these lines likely involves pre-incision events or the excision step, but not the incision, polymerization, or ligation steps; and (iv) at least four functional complementation groups for mismatch repair may be involved in human cancer.

Cell Line↗