Structural insights into yeast DNA polymerase delta by small angle X-ray scattering

DNA polymerase delta (Poldelta) is a multisubunit polymerase that plays an indispensable role in replication from yeast to humans. Poldelta from Saccharomyces cerevisiae is composed of three subunits: Pol3, Pol31, and Pol32. Despite the elucidation of the structures and models of the individual subunits (or portions, thereof), the nature of their assembly remains unclear. We present here a small-angle X-ray scattering analysis of a yeast Poldelta complex (Poldelta(T)) composed of Pol3, Pol31, and Pol32N (amino acids 1-103 of Pol32). From the small angle X-ray scattering global parameters and reconstructed envelopes, we show that Poldelta(T) adopts an elongated conformation with a radius of gyration (R(g)) of approximately 52 A and a maximal dimension of approximately 190 A. We also propose an orientation for the accessory Pol31-Pol32N subunits relative to the Pol3 catalytic core that best agrees with the experimental scattering profile. The analysis also points to significant conformational variability that may allow Poldelta to better coordinate its action with other proteins at the replication fork.

Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta

DNA polymerase δ (Polδ) is a high fidelity polymerase that plays a central role in replication from yeast to humans. We present here the crystal structure of the catalytic subunit of yeast Polδ in ternary complex with a template-primer and an incoming nucleotide. The structure, determined at 2.0Å resolution, catches the enzyme in the act of replication. The structure reveals how the polymerase and exonuclease domains are juxtaposed relative to each other and how a correct nucleotide is selected and incorporated. The structure also reveals the “sensing” interactions near the primer terminus that signal a switch from the polymerizing to the editing mode. Taken together, the structure provides a chemical basis for the bulk of DNA synthesis in eukaryotic cells and a framework for understanding the effects of mutations in Polδ̣ that cause cancers.

Structure of the human Rev1-DNA-dNTP ternary complex

Y-family DNA polymerases have proven to be remarkably diverse in their functions and in strategies for replicating through DNA lesions. The structure of yeast Rev1 ternary complex has revealed the most radical replication strategy, where the polymerase itself dictates the identity of the incoming nucleotide, as well as the identity of the templating base. We show here that many of the key elements of this highly unusual strategy are conserved between yeast and human Rev1, including the eviction of template G from the DNA helix and the pairing of incoming deoxycytidine 5'-triphosphate with a surrogate arginine residue. We also show that the catalytic core of human Rev1 is uniquely augmented by two large inserts, I1 and I2, wherein I1 extends >20 A away from the active site and may serve as a platform for protein-protein interactions specific for Rev1's role in translesion DNA synthesis in human cells, and I2 acts as a "flap" on the hydrophobic pocket accommodating template G. We suggest that these novel structural features are important for providing human Rev1 greater latitude in promoting efficient and error-free translesion DNA synthesis through the diverse array of bulky and potentially carcinogenic N(2)-deoxyguanosine DNA adducts in human cells.

DNA synthesis across an abasic lesion by human DNA polymerase iota

Abasic sites are among the most abundant DNA lesions formed in human cells, and they present a strong block to replication. DNA polymerase iota (Poliota) is one of the few DNA Pols that does not follow the A-rule opposite an abasic site. We present here three structures of human Poliota in complex with DNAs containing an abasic lesion and dGTP, dTTP, or dATP as the incoming nucleotide. The structures reveal a mechanism of translesion synthesis across an abasic lesion that differs from that in other Pols. Both the abasic lesion and the incoming dNTPs are intrahelical and are closely apposed across a constricted active site cleft. The dNTPs partake in distinct networks of hydrogen bonds in the "void" opposite the lesion. These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Poliota's small preference for insertion of dGTP over other nucleotides opposite this common lesion.

Yeast Rev1 protein promotes complex formation of DNA polymerase zeta with Pol32 subunit of DNA polymerase delta

Yeast DNA polymerase (Pol) delta, essential for DNA replication, is comprised of 3 subunits, Pol3, Pol31, and Pol32. Of these, the catalytic subunit Pol3 and the second subunit Pol31 are essential, whereas the Pol32 subunit is not essential for DNA replication. Although Pol32 is an integral component of Pol delta, it is also required for translesion synthesis (TLS) by Pol zeta. To begin to decipher the bases of Pol32 involvement in Pol zeta-mediated TLS, here we examine whether Pol32 physically interacts with Pol zeta or its associated proteins and provide evidence for the physical interaction of Pol32 with Rev1. Rev1 plays an indispensable structural role in Pol zeta-mediated TLS and it binds the Rev3 catalytic subunit of Pol zeta. Here, we show that although Pol32 does not directly bind Pol zeta, Pol32 can bind the Rev1-Pol zeta complex through its interaction with Rev1. We find that Pol32 binding has no stimulatory effect on DNA synthesis either by Rev1 in the Rev1-Pol32 complex or by Pol zeta in the Pol zeta-Rev1-Pol32 complex, irrespective of whether proliferating cell nuclear antigen has been loaded onto DNA or not. We discuss evidence for the biological significance of Rev1 binding to Pol32 for Pol zeta function in TLS and suggest a structural role for Rev1 in modulating the binding of Pol zeta with Pol32 in Pol delta stalled at a lesion site.

Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion

Background

Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polκ) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polκ's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polκ in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide.

Methodology and Principal Findings

We show that the Polκ active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP.

Conclusions and Significance

The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polκ is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polκ is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.

Sputtering and heating of Titan's upper atmosphere

Titan is an important endpoint for understanding atmospheric evolution. Prior to Cassini's arrival at Saturn, modelling based on Voyager data indicated that the hydrogen escape rate was large (1-3x1028amus-1), but the escape rates for carbon and nitrogen species were relatively small (5x1026amus-1) and dominated by atmospheric sputtering. Recent analysis of the structure of Titan's thermosphere and corona attained from the Ion and Neutral Mass Spectrometer and the Huygens Atmospheric Structure Instrument on Cassini have led to substantially larger estimates of the loss rate for heavy species (0.3-5x1028amus-1). At the largest rate suggested, a mass that is a significant fraction of the present atmosphere would have been lost to space in 4Gyr; hence, understanding the nature of the processes driving escape is critical. The recent estimates of neutral escape are reviewed here, with particular emphasis on plasma-induced sputtering and heating. Whereas the loss of hydrogen is clearly indicated by the altitude dependence of the H2 density, three different one-dimensional models were used to estimate the heavy-molecule loss rate using the Cassini data for atmospheric density versus altitude. The solar heating rate and the nitrogen density profile versus altitude were used in a fluid dynamic model to extract an average net upward flux below the exobase; the diffusion of methane through nitrogen was described below the exobase using a model that allowed for outward flow; and the coronal structure above the exobase was simulated by presuming that the observed atmospheric structure was due to solar- and plasma-induced hot particle production. In the latter, it was hypothesized that hot recoils from photochemistry or plasma-ion-induced heating were required. In the other two models, the upward flow extracted is driven by heat conduction from below, which is assumed to continue to act above the nominal exobase, producing a process referred to as 'slow hydrodynamic' escape. These models and the resulting loss rates are reviewed and compared. It is pointed out that preliminary estimates of the composition of the magnetospheric plasma at Titan's orbit appear to be inconsistent with the largest loss rates suggested for the heavy species, and the mean upward flow extracted in the one-dimensional models could be consistent with atmospheric loss by other mechanisms or with transport to other regions of Titan's atmosphere.

An electronic linkage system for health behavior counseling effect on delivery of the 5A's

BACKGROUND

A variety of factors limit the ability of clinicians to offer intensive counseling to patients with unhealthy behaviors, and few patients (2%-5%) are referred to the community counseling resources that do offer such assistance. A system that could increase referrals through an efficient collaborative partnership between community programs and clinicians could have major public health implications; such was the subject of this feasibility evaluation.

METHODS

At nine primary care practices, an electronic linkage system (eLinkS) was instituted to promote health behavior counseling and to automate patient referrals to community counseling services. Patients were offered 9 months of free counseling for weight loss, smoking cessation, and problem drinking at a choice of venues: group counseling, telephone counseling, computer care, and usual care. The delivery of behavioral counseling, measured by the 5A's (ask, address, advise, assess, agree, arrange) and patients' reported experiences with eLinkS, was examined.

RESULTS

For 5 weeks eLinkS was used, until high referral volumes depleted counseling funds. Of the 5679 patients visiting the practices, 71% had an unhealthy behavior. Of these patients, 10% were referred for intensive counseling from a community program, most often for weight loss. Counseling and referrals occurred regardless of visit type--wellness, acute, or chronic care. eLinkS was used more often for middle-aged adults and women and by more-experienced clinicians.

CONCLUSIONS

The intervention increased the rate at which patients were referred for intensive behavioral counseling compared to current practice norms. Given the evidence that intensive counseling is more effective in promoting behavior change, implementing eLinkS could have substantial public health benefits.

The health impact of resolving racial disparities: an analysis of US mortality data

The US health system spends far more on the "technology" of care (e.g., drugs, devices) than on achieving equity in its delivery. For 1991 to 2000, we contrasted the number of lives saved by medical advances with the number of deaths attributable to excess mortality among African Americans. Medical advances averted 176 633 deaths, but equalizing the mortality rates of Whites and African Americans would have averted 886202 deaths. Achieving equity may do more for health than perfecting the technology of care.

Correlations of maternal buprenorphine dose, buprenorphine, and metabolite concentrations in meconium with neonatal outcomes

For the first time, relationships among maternal buprenorphine dose, meconium buprenorphine and metabolite concentrations, and neonatal outcomes are reported. Free and total buprenorphine and norbuprenorphine, nicotine, opiates, cocaine, benzodiazepines, and metabolites were quantified in meconium from 10 infants born to women who had received buprenorphine during pregnancy. Neither cumulative nor total third-trimester maternal buprenorphine dose predicted meconium concentrations or neonatal outcomes. Total buprenorphine meconium concentrations and buprenorphine/norbuprenorphine ratios were significantly related to neonatal abstinence syndrome (NAS) scores >4. As free buprenorphine concentration and percentage free buprenorphine increased, head circumference decreased. Thrice-weekly urine tests for opiates, cocaine, and benzodiazepines and self-reported smoking data from the mother were compared with data from analysis of the meconium to estimate in utero exposure. Time of last drug use and frequency of use during the third trimester were important factors associated with drug-positive meconium specimens. The results suggest that buprenorphine and metabolite concentrations in the meconium may predict the onset and frequency of NAS.

Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase

Acrolein is generated as the end product of lipid peroxidation and is also a ubiquitous environmental pollutant. Its reaction with the N2 of guanine leads to a cyclic gamma-HOPdG adduct that presents a block to normal replication. We show here that yeast Rev1 incorporates the correct nucleotide C opposite a permanently ring-closed form of gamma-HOPdG (PdG) with nearly the same efficiency as opposite an undamaged G. The structural basis of this action lies in the eviction of the PdG adduct from the Rev1 active site, and the pairing of incoming dCTP with a "surrogate" arginine residue. We also show that yeast Polzeta can carry out the subsequent extension reaction. Together, our studies reveal how the exocyclic PdG adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Rev1 and Polzeta provides for accurate and efficient synthesis through this potentially carcinogenic DNA lesion.

Patient perceptions of how physicians communicate during prostate cancer screening discussions: a comparison of residents and faculty

BACKGROUND

Residents are required to demonstrate competency in communication skills. Prostate cancer screening discussions are examples of complex physician-patient communication processes, requiring an objective presentation of the known risks, potential benefits, and scientific uncertainties surrounding screening. National organizations recommend shared decision making (SDM) in these discussions.

METHODS

A stratified analysis to contrast resident and faculty outcomes was planned as part of a randomized controlled trial comparing decision aids for prostate cancer screening in a suburban Washington, DC, residency practice. All eligible men between the ages of 50 and 70 years scheduled for a wellness examination with either a resident or a faculty physician were randomly assigned to one of two intervention arms (Web- or paper-based decision aid) or to the control group (no pre-visit education). Patients were asked to complete exit surveys that evaluated their perceptions of key elements of SDM for prostate cancer screening (PCS).

RESULTS

Patients seen by resident physicians were younger than patients seen by faculty, and a smaller proportion had undergone previous prostate-specific antigen (PSA) testing. Patients seen by residents and faculty reported similar levels of the elements of SDM (eg, knowledge about PCS, achieving their desired locus of control for the decision) and similar time spent discussing screening. Both groups also had nearly identical decisional conflict scores and PSA testing rates. Residents discussed more PCS topics (6.3 versus 5.3 topics), including more topics that might influence a patient to decide against screening, than did faculty physicians.

CONCLUSIONS

According to patient perceptions, residents appeared to perform as well as faculty in SDM and other aspects of PCS discussions, although the topics that they covered with patients might have differed.

Effect on cessation counseling of documenting smoking status as a routine vital sign: an ACORN study

PURPOSE

Guidelines encourage primary care clinicians to document smoking status when obtaining patients' blood pressure, temperature, and pulse rate (vital signs), but whether this practice promotes cessation counseling is unclear. We examined whether the vital sign intervention influences patient-reported frequency and intensity of tobacco cessation counseling.

METHODS

This study was a cluster-randomized, controlled trial conducted in the Virginia Ambulatory Care Outcomes Research Network (ACORN). At intervention practices, nurses and medical assistants were instructed to assess the tobacco use status of every adult patient and record it with the traditional vital signs. Control practices did not use any systematic tobacco screening or identification system. Outcomes were the proportion of smokers reporting clinician counseling of any kind and the frequency of 2 counseling subcomponents: simple quit advice and more intensive discussion.

RESULTS

A total of 6,729 adult patients (1,149 smokers) at 18 primary care practices completed exit questionnaires during a 6-month comparison period. Among 561 smokers at intervention practices, 61.9% reported receiving any counseling, compared with 53.4% of the 588 smokers at control practices, for a difference of 8.6% (P = .04). The effect was largely restricted to simple advice, which was reported by 59.9% of intervention patients and 51.5% of control patients (P=.04). There was no significant increase in more extensive discussion, with 32.5% and 29.3% of patients at intervention and control practices, respectively, reporting this type of counseling (P=.18).

CONCLUSIONS

The vital sign intervention promotes tobacco counseling at primary care practices through a modest increase in simple advice to quit. When implemented as a stand-alone intervention, it does not appear to increase intensive counseling.

A role for yeast and human translesion synthesis DNA polymerases in promoting replication through 3-methyl adenine

3-Methyl adenine (3meA), a minor-groove DNA lesion, presents a strong block to synthesis by replicative DNA polymerases (Pols). To elucidate the means by which replication through this DNA lesion is mediated in eukaryotic cells, here we carry out genetic studies in the yeast Saccharomyces cerevisiae treated with the alkylating agent methyl methanesulfonate. From the studies presented here, we infer that replication through the 3meA lesion in yeast cells can be mediated by the action of three Rad6-Rad18-dependent pathways that include translesion synthesis (TLS) by Pol(eta) or -zeta and an Mms2-Ubc13-Rad5-dependent pathway which presumably operates via template switching. We also express human Pols iota and kappa in yeast cells and show that they too can mediate replication through the 3meA lesion in yeast cells, indicating a high degree of evolutionary conservation of the mechanisms that control TLS in yeast and human cells. We discuss these results in the context of previous observations that have been made for the roles of Pols eta, iota, and kappa in promoting replication through the minor-groove N2-dG adducts.

Gonorrhea and chlamydia in the United States among persons 14 to 39 years of age, 1999 to 2002

BACKGROUND

Nationally representative surveys of chlamydia and gonorrhea are an important measure of disease burden and progress of screening programs.

OBJECTIVE

To measure chlamydia and gonorrhea prevalence in the United States.

DESIGN

Analysis of sexual history information and urine specimens collected in the National Health and Nutrition Examination Survey (NHANES), 1999-2002.

SETTING

U.S. civilian noninstitutionalized population as sampled by NHANES, 1999-2002.

PARTICIPANTS

6632 NHANES respondents.

MEASUREMENTS

Urine specimens were tested for chlamydia and gonorrhea. Results were weighted to represent the U.S. civilian, noninstitutionalized population between 14 and 39 years of age.

RESULTS

Prevalence of gonorrheal infection was 0.24% (95% CI, 0.16% to 0.38%). Prevalence of gonorrheal infection was higher among non-Hispanic black persons (1.2% [CI, 0.7% to 1.9%]) than among non-Hispanic white persons (0.07% [CI, 0.02% to 0.24%]). Among those with gonorrheal infection, 46% also had chlamydial infection. Prevalence of chlamydial infection was 2.2% (CI, 1.8% to 2.8%) and was similar between males (2.0% [CI, 1.6% to 2.5%]) and females (2.5% [CI, 1.8% to 3.4%]). Among females, the highest prevalence was in those age 14 to 19 years, whereas among males, it was highest in those age 14 to 29 years. Prevalence was higher among non-Hispanic black persons (6.4% [CI, 5.4% to 7.5%]) than non-Hispanic white persons (1.5% [CI, 1.0% to 2.4%]). Among females with a history of gonorrhea or chlamydia in the previous 12 months, chlamydia prevalence was 16.7% (CI, 5.5% to 50.7%).

LIMITATIONS

The specificity of urine-based assays for chlamydia and gonorrhea is limited, and the possible misclassification of sexual experience status may have affected the accuracy of some estimates.

CONCLUSIONS

The findings support current recommendations to screen sexually active females age 25 years or younger for chlamydia, to retest infected females for chlamydial infection, and to co-treat individuals with gonorrhea for chlamydia.

Generalized approach to Ewald sums

We derive Ewald sum formulas for potential energy and force for a system of point charges interacting with an arbitrary, long-range central potential. The system is made neutral by a uniform background of opposite charge interacting with the same potential. These formulas can be readily used in computer numerical simulations of model physical systems. In particular, expressions for the potential energy and the force have been obtained in both two and three dimensions for Coulomb and other power-law potentials, Yukawa systems, and for an electronic bilayer. We discuss numerical results and their accuracy for various systems and, based on our analysis, suggest values to be used for the parameters that appear in the Ewald sums.

Human DNA polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass

Human DNA polymerase kappa (Pol kappa) is a proficient extender of mispaired primer termini on undamaged DNAs and is implicated in the extension step of lesion bypass. We present here the structure of Pol kappa catalytic core in ternary complex with DNA and an incoming nucleotide. The structure reveals encirclement of the DNA by a unique "N-clasp" at the N terminus of Pol kappa, which augments the conventional right-handed grip on the DNA by the palm, fingers, and thumb domains and the PAD and provides additional thermodynamic stability. The structure also reveals an active-site cleft that is constrained by the close apposition of the N-clasp and the fingers domain, and therefore can accommodate only a single Watson-Crick base pair. Together, DNA encirclement and other structural features help explain Pol kappa's ability to extend mismatches and to promote replication through various minor groove DNA lesions, by extending from the nucleotide incorporated opposite the lesion by another polymerase.

Patient education on prostate cancer screening and involvement in decision making

PURPOSE

Many clinicians lack resources to engage patients in shared decision making for prostate cancer screening. We sought to evaluate whether previsit educational decision aids facilitate shared decision making.

METHODS

This randomized controlled study compared a Web-based and a paper-based decision aid with no previsit education. Men aged 50 to 70 years undergoing a health maintenance examination at a large family practice were enrolled. The primary outcome was patient-reported level of control over the decision to be screened. Secondary outcomes included frequency of screening, patient knowledge, decisional conflict, and time spent discussing screening.

RESULTS

A total of 497 men participated (75 control, 196 brochure, 226 Web site). Patients exposed to either aid were no more likely than control patients to report a collaborative decision: 36% of patients in each group reported equally sharing decision responsibility. Exposure to either decision aid increased patients' involvement in decision making compared with the control condition (Web site, P = .03; brochure, P = .03). Only 46% of control patients reported an active decision-making role, compared with 56% of Web site and 54% of brochure patients. Patients exposed to a decision aid answered a greater percentage of knowledge questions correctly (54% control vs 69% Web site, P <.001, and vs 69% brochure, P <.001) and were less likely to be screened (94% control vs 86% Web site, P = .06, and vs 85% brochure, P = .04).

CONCLUSIONS

Patients in the decision aid groups were more informed and more engaged in the screening decision than their control counterparts. Exposure did not promote shared decision-making control, however. Whether shared decision making is the ideal model and how to measure its occurrence are subjects for further research.

How physicians approach prostate cancer screening before and after losing a lawsuit

PURPOSE

In 2004, a commentary by Merenstein was published in JAMA describing how he was sued for engaging a patient in shared decision making for prostate cancer screening. The article sparked considerable debate on the impact of litigation on medical care. A natural experiment (a study assessing shared decision making under way at the practice that was sued) enabled us to evaluate whether physicians changed their prostate cancer screening behavior after the lawsuit.

METHODS

As part of a randomized controlled trial conducted between January 2002 and November 2004, patients and physicians completed exit questionnaires about prostate cancer screening discussions after health maintenance examinations. We compared responses before, during, and after physicians became aware of the lawsuit.

RESULTS

A total of 432 of 497 patients completed questionnaires (180 before the practice became aware of the lawsuit, 87 as knowledge of the case diffused through the practice, and 165 after publication of Merenstein's commentary). Comparing patients' responses over the 3 time periods, there were no changes in the average locus of decision-making control, time spent discussing screening, number of screening topics discussed, knowledge scores, or decisional conflict. The frequency with which physicians reported performing prostate-specific antigen testing increased (before vs after: 84% vs 90%; P = .03), and physicians were more likely to report that they, rather than the patients, had made the screening decision (before vs after: 3.3% vs 11.1%; P = .003).

CONCLUSIONS

The physicians in closest proximity to this well-known legal case continued to engage patients in shared decision making and to let patients decide whether to be screened. Prostate-specific antigen testing increased during this period.

Giving everyone the health of the educated: an examination of whether social change would save more lives than medical advances

OBJECTIVES

Social determinants of health, such as inadequate education, contribute greatly to mortality rates. We examined whether correcting the social conditions that account for excess deaths among individuals with inadequate education might save more lives than medical advances (e.g., new drugs and devices).

METHODS

Using US vital statistics data for 1996 through 2002, we applied indirect standardization techniques to estimate the maximum number of averted deaths attributable to medical advances and the number of deaths that would have been averted if mortality rates among adults with lesser education had been the same as those among college-educated adults.

RESULTS

Medical advances averted a maximum of 178193 deaths during the study period. Correcting disparities in education-associated mortality rates would have saved 1369335 lives during the same period, a ratio of 8:1.

CONCLUSIONS

Higher mortality rates among individuals with inadequate education reflect a complex causal pathway and the influence of confounding variables. Formidable efforts at social change would be necessary to eliminate disparities, but the changes would save more lives than would society's current heavy investment in medical advances. Spending large sums of money on such advances at the expense of social change may be jeopardizing public health.

Human DNA polymerase kappa forms nonproductive complexes with matched primer termini but not with mismatched primer termini

Human DNA polymerase kappa (pol kappa) is a member of the Y family of DNA polymerases that function in translesion synthesis. It synthesizes DNA with moderate fidelity and does not efficiently incorporate nucleotides opposite DNA lesions. Pol kappa has the unusual ability to efficiently extend from mismatched primer termini, and it extends readily from nucleotides inserted by other DNA polymerases opposite a variety of DNA lesions. All of this has suggested that pol kappa functions during the extension step of translesion synthesis. Here, we have carried out pre-steady-state kinetic studies of pol kappa using DNA with matched and mismatched primer termini. Interestingly, we find that mismatches present only a modest kinetic barrier to nucleotide incorporation by pol kappa. Moreover, and quite surprisingly, active-site titrations revealed that the concentration of active pol kappa is very low with matched DNA, and from DNA trapping experiments we determined that this was due to the formation of nonproductive protein.DNA complexes. In marked contrast, we found that the concentration of active pol kappa was six-fold greater with mismatched DNA than with matched DNA. Thus, pol kappa forms nonproductive complexes with matched but not with mismatched DNA. From these observations, we conclude that pol kappa has evolved to specifically function on DNA substrates with aberrant primer-terminal base pairs, such as the ones it would encounter during the extension step of translesion synthesis.

Complex formation with Rev1 enhances the proficiency of Saccharomyces cerevisiae DNA polymerase zeta for mismatch extension and for extension opposite from DNA lesions

Rev1, a Y family DNA polymerase (Pol) functions together with Polzeta, a B family Pol comprised of the Rev3 catalytic subunit and Rev7 accessory subunit, in promoting translesion DNA synthesis (TLS). Extensive genetic studies with Saccharomyces cerevisiae have indicated a requirement of both Polzeta and Rev1 for damage-induced mutagenesis, implicating their involvement in mutagenic TLS. Polzeta is specifically adapted to promote the extension step of lesion bypass, as it proficiently extends primer termini opposite DNA lesions, and it is also a proficient extender of mismatched primer termini on undamaged DNAs. Since TLS through UV-induced lesions and various other DNA lesions does not depend upon the DNA-synthetic activity of Rev1, Rev1 must contribute to Polzeta-dependent TLS in a nonenzymatic way. Here, we provide evidence for the physical association of Rev1 with Polzeta and show that this binding is mediated through the C terminus of Rev1 and the polymerase domain of Rev3. Importantly, a rev1 mutant that lacks the C-terminal 72 residues which inactivate interaction with Rev3 exhibits the same high degree of UV sensitivity and defectiveness in UV-induced mutagenesis as that conferred by the rev1Delta mutation. We propose that Rev1 binding to Polzeta is indispensable for the targeting of Polzeta to the replication fork stalled at a DNA lesion. In addition to this structural role, Rev1 binding enhances the proficiency of Polzeta for the extension of mismatched primer termini on undamaged DNAs and for the extension of primer termini opposite DNA lesions.

Mms2-Ubc13-dependent and -independent roles of Rad5 ubiquitin ligase in postreplication repair and translesion DNA synthesis in Saccharomyces cerevisiae

The Rad6-Rad18 ubiquitin-conjugating enzyme complex of Saccharomyces cerevisiae promotes replication through DNA lesions via three separate pathways that include translesion synthesis (TLS) by DNA polymerases eta and zeta and postreplicational repair (PRR) of discontinuities that form in the newly synthesized DNA opposite from DNA lesions, mediated by the Mms2-Ubc13 ubiquitin-conjugating enzyme and Rad5. Rad5 is an SWI/SNF family ATPase, and additionally, it functions as a ubiquitin ligase in the ubiquitin conjugation reaction. To decipher the roles of these Rad5 activities in lesion bypass, here we examine the effects of mutations in the Rad5 ATPase and ubiquitin ligase domains on the PRR of UV-damaged DNA and on UV-induced mutagenesis. Even though the ATPase-defective mutation confers only a modest degree of UV sensitivity whereas the ubiquitin ligase mutation causes a high degree of UV sensitivity, we find that both of these mutations produce the same high level of PRR defect as that conferred by the highly UV-sensitive rad5Delta mutation. From these studies, we infer a requirement of the Rad5 ATPase and ubiquitin ligase activities in PRR, and based upon the effects of different rad5 mutations on UV mutagenesis, we suggest a role for Rad5 in affecting the efficiency of lesion bypass by the TLS polymerases. In contrast to the role of Rad5 in PRR, however, where its function is coupled with that of Mms2-Ubc13, Rad5 function in TLS would be largely independent of this ubiquitin-conjugating enzyme complex.

The rising prevalence of severe poverty in America: a growing threat to public health

BACKGROUND

The U.S. poverty rate has increased since 2000, but the depth of poverty experienced by Americans has been inadequately studied. Of particular concern is whether severe poverty is increasing, a trend that would carry important public health implications.

METHODS

Income-to-poverty (I/P) ratios and income deficits/surpluses were examined for the 1990-2004 period. The severely poor, moderately poor, and near-poor were classified as those with I/P ratios of less than 0.5, 0.5 to 1.0, or 1.0 to 2.0, respectively. Income deficits/surpluses were classified relative to the poverty threshold as Tier I (deficit Dollars 8000 or more), Tier II (deficit or surplus less than Dollars 8000), or Tier III (surplus more than Dollars 8000). Odds ratios for severe poverty and Tier I were also calculated.

RESULTS

Severe poverty increased between 2000 and 2004-those with I/P ratios of less than 0.5 grew by 20%, and Tier I grew by 45% to 55%-while the prevalence of higher levels of income diminished. The population in severe poverty was over-represented by children (odds ratio [OR] = 1.69, confidence interval [CI] = 1.63-1.75), African Americans (OR = 2.84, CI = 2.74-2.95), and Hispanics (OR = 1.64, CI = 1.58-1.71).

CONCLUSIONS

From 2000 to 2004, the prevalence of severe poverty increased sharply while the proportion of Americans in higher income tiers diminished. These trends have broad societal implications. Likely health consequences include a higher prevalence of chronic illnesses, more frequent and severe disease complications, and increased demands and costs for healthcare services. Adverse effects on children warrant special concern. The growth in the number of Americans living in poverty calls for the re-examination of policies enacted in recent years to foster economic progress.

Role of hoogsteen edge hydrogen bonding at template purines in nucleotide incorporation by human DNA polymerase iota

Human DNA polymerase iota (Pol iota) differs from other DNA polymerases in that it exhibits a marked template specificity, being more efficient and accurate opposite template purines than opposite pyrimidines. The crystal structures of Pol iota with template A and incoming dTTP and with template G and incoming dCTP have revealed that in the Pol iota active site, the templating purine adopts a syn conformation and forms a Hoogsteen base pair with the incoming pyrimidine which remains in the anti conformation. By using 2-aminopurine and purine as the templating residues, which retain the normal N7 position but lack the N(6) of an A or the O(6) of a G, here we provide evidence that whereas hydrogen bonding at N(6) is dispensable for the proficient incorporation of a T opposite template A, hydrogen bonding at O(6) is a prerequisite for C incorporation opposite template G. To further analyze the contributions of O(6) and N7 hydrogen bonding to DNA synthesis by Pol iota, we have examined its proficiency for replicating through the (6)O-methyl guanine and 8-oxoguanine lesions, which affect the O(6) and N7 positions of template G, respectively. We conclude from these studies that for proficient T incorporation opposite template A, only the N7 hydrogen bonding is required, but for proficient C incorporation opposite template G, hydrogen bonding at both the N7 and O(6) is an imperative. The dispensability of N(6) hydrogen bonding for proficient T incorporation opposite template A has important biological implications, as that would endow Pol iota with the ability to replicate through lesions which impair the Watson-Crick hydrogen bonding potential at both the N1 and N(6) positions of templating A.

Alcohol Withdrawal Pharmacotherapy for Inpatients with Medical Comorbidity

Studies show that symptom-triggered dosing is best for treatment of alcohol withdrawal in patients on chemical dependence wards without other illness. On general medical hospital wards, withdrawal may be affected by comorbid medical illness. A clinical trial was undertaken to determine whether there is a difference between symptom-triggered (ST) and fixed-schedule (FS) dosing of lorazepam in patients hospitalized on general medical wards at a university medical center. One hundred eighty-three subjects were assessed by their nurses with the Revised Clinical Institute Withdrawal Assessment for Alcohol (CIWA-Ar) scale. Subjects in the ST arm received lorazepam doses based on CIWA-Ar score. Subjects in the FS arm received scheduled lorazepam with tapering over 4 days. Symptom-triggered dosing for alcohol withdrawal for general medicine inpatients results in less lorazepam given with similar reduction in CIWA-Ar scores for the first 2 days, but a higher proportion of protocol errors.

An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site

Substrate-induced conformational change of the protein is the linchpin of enzymatic reactions. Replicative DNA polymerases, for example, convert from an open to a closed conformation in response to dNTP binding. Human DNA polymerase-iota (hPoliota), a member of the Y family of DNA polymerases, differs strikingly from other polymerases in its much higher proficiency and fidelity for nucleotide incorporation opposite template purines than opposite template pyrimidines. We present here a crystallographic analysis of hPoliota binary complexes, which together with the ternary complexes show that, contrary to replicative DNA polymerases, the DNA, and not the polymerase, undergoes the primary substrate-induced conformational change. The incoming dNTP "pushes" templates A and G from the anti to the syn conformation dictated by a rigid hPoliota active site. Together, the structures posit a mechanism for template selection wherein dNTP binding induces a conformational switch in template purines for productive Hoogsteen base pairing.

Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota

The 1,N6-ethenodeoxyadenosine (epsilon dA) lesion is promutagenic and has been implicated in carcinogenesis. We show here that human Pol iota, a Y-family DNA polymerase, can promote replication through this lesion by proficiently incorporating a nucleotide opposite it. The structural basis of this action is rotation of the epsilon dA adduct to the syn conformation in the Pol iota active site and presentation of its 'Hoogsteen edge' for hydrogen-bonding with incoming dTTP or dCTP. We also show that Pol zeta carries out the subsequent extension reaction and that efficiency of extension from epsilon dA x T is notably higher than from epsilon dA x C. Together, our studies reveal for the first time how the exocyclic epsilon dA adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Pol iota and Pol zeta provides for efficient and error-free synthesis through this potentially carcinogenic DNA lesion.

Replication past a trans-4-hydroxynonenal minor-groove adduct by the sequential action of human DNA polymerases iota and kappa

The X-ray crystal structure of human DNA polymerase iota (Poliota) has shown that it differs from all known Pols in its dependence upon Hoogsteen base pairing for synthesizing DNA. Hoogsteen base pairing provides an elegant mechanism for synthesizing DNA opposite minor-groove adducts that present a severe block to synthesis by replicative DNA polymerases. Germane to this problem, a variety of DNA adducts form at the N2 minor-groove position of guanine. Previously, we have shown that proficient and error-free replication through the gamma-HOPdG (gamma-hydroxy-1,N2-propano-2'-deoxyguanosine) adduct, which is formed from the reaction of acrolein with the N2 of guanine, is mediated by the sequential action of human Poliota and Polkappa, in which Poliota incorporates the nucleotide opposite the lesion site and Polkappa carries out the subsequent extension reaction. To test the general applicability of these observations to other adducts formed at the N2 position of guanine, here we examine the proficiency of human Poliota and Polkappa to synthesize past stereoisomers of trans-4-hydroxy-2-nonenal-deoxyguanosine (HNE-dG). Even though HNE- and acrolein-modified dGs share common structural features, due to their increased size and other structural differences, HNE adducts are potentially more blocking for replication than gamma-HOPdG. We show here that the sequential action of Poliota and Polkappa promotes efficient and error-free synthesis through the HNE-dG adducts, in which Poliota incorporates the nucleotide opposite the lesion site and Polkappa performs the extension reaction.

Effect of statins and white blood cell count on mortality in patients with ischemic left ventricular dysfunction undergoing percutaneous coronary intervention

BACKGROUND

While morbidity and mortality were shown to be increased in the setting of an elevated white blood cell (WBC) count for patients with acute coronary syndrome, the impact of statin therapy on mortality for patients with an elevated WBC count is unknown in high-risk patients with coronary artery disease.

HYPOTHESIS

The goal of this study was to determine whether statin therapy improved survival in patients with elevated WBC count undergoing percutaneous coronary intervention (PCI) with preexisting left ventricular (LV) dysfunction, a population at high risk for adverse outcomes.

METHODS

We retrospectively evaluated consecutive patient procedures performed at our institution from 1996 through 1999. Patients had a technically adequate angiographic left ventriculogram with a calculated ejection fraction (EF) < or = 50%. Patients with prior coronary artery bypass graft were excluded. Mortality data were retrieved using the U.S. Social Security Death Index. Follow-up ranged from 3.5 to 6.5 years. Means are provided with +/- standard deviation, and p values < 0.05 were considered significant.

RESULTS

Of the study population of 238 patients (average EF 39 +/- 9.8%, mean age 57.5 +/- 12 years, 68% men) 61% underwent PCI for a recent myocardial infarction, 68% received stents, and 65% were discharged on statins. Mean WBC count was 9,000 +/- 3,100 cells/mm3, with 28% of patients having a WBC > or = 10,000 cells/mm3. During follow-up, 27% of our population died. Patients with a WBC > or = 10,000 had worse survival than patients with WBC < 10,000 (1-year survival: 86 vs. 96%, p < 0.05; 3-year survival: 79 vs. 89%, p < 0.05). Survival was significantly improved in patients on statin therapy regardless of WBC count, but the greatest benefit tended to be in patients with WBC > or = 10,000 (WBC > or = 10,000; odds ratio [OR] 5.14, 95% confidence interval [CI] 1.44-19.0, WBC < 10,000; OR 2.79,95% CI 1.13-7.1). Proportional hazard regression analysis demonstrated that both statin therapy and WBC count predicted mortality.

CONCLUSION

Patients undergoing PCI with LV dysfunction discharged on statins had improved survival regardless of WBC count, with a trend for greater improvement in patients with elevated WBC counts. In addition, WBC count predicts mortality in this high-risk population with LV dysfunction undergoing PCI.

The Interaction of the Atmosphere of Enceladus with Saturn's Plasma

During the 14 July 2005 encounter of Cassini with Enceladus, the Cassini Plasma Spectrometer measured strong deflections in the corotating ion flow, commencing at least 27 Enceladus radii (27 x 252.1 kilometers) from Enceladus. The Cassini Radio and Plasma Wave Science instrument inferred little plasma density increase near Enceladus. These data are consistent with ion formation via charge exchange and pickup by Saturn's magnetic field. The charge exchange occurs between neutrals in the Enceladus atmosphere and corotating ions in Saturn's inner magnetosphere. Pickup ions are observed near Enceladus, and a total mass loading rate of about 100 kilograms per second (3 x 10(27) H(2)O molecules per second) is inferred.

A practice-sponsored Web site to help patients pursue healthy behaviors: an ACORN study

PURPOSE

We tested whether patients are more likely to pursue healthy behaviors (eg, physical activity, smoking cessation) if referred to a tailored Web site that provides valuable information for behavior change.

METHODS

In a 9-month pre-post comparison with nonrandomized control practices, 6 family practices (4 intervention, 2 control) encouraged adults with unhealthy behaviors to visit the Web site. For patients from intervention practices, the Web site offered tailored health advice, a library of national and local resources, and printouts for clinicians. For patients from control practices, the Web site offered static information pages. Patient surveys assessed stage of change and health behaviors at baseline and follow-up (at 1 and 4 months), Web site use, and satisfaction.

RESULTS

During the 9 months, 932 patients (4% of adults attending the practice) visited the Web site, and 273 completed the questionnaires. More than 50% wanted physician assistance with health behaviors. Stage of change advanced and health behaviors improved in both intervention and control groups. Intervention patients reported greater net improvements at 1 month, although the differences approached significance only for physical activity and readiness to change dietary fat intake. Patients expressed satisfaction with the Web site but wished it provided more detailed information and greater interactivity with clinicians.

CONCLUSIONS

Clinicians face growing pressure to offer patients good information on health promotion and other health care topics. Referring patients to a well-designed Web site that offers access to the world's best information is an appealing alternative to offering handouts or impromptu advice. Interactive Web sites can facilitate behavior change and can interface with electronic health records. Determining whether referral to an informative Web site improves health outcomes is a methodological challenge, but the larger question is whether information alone is sufficient to promote behavior change. Web sites are more likely to be effective as part of a suite of tools that incorporate personal assistance.

Effect of specimen order on Chlamydia trachomatis and Neisseria gonorrhoeae test performance and adequacy of Papanicolaou smear

STUDY OBJECTIVE

To evaluate the effect of specimen collection order on the performance of diagnostic tests for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC), and the specimen adequacy of ThinPrep Papanicolaou (Pap) smears.

DESIGN

Prospective cohort study.

SETTING

Public adolescent clinic.

POPULATION

313 women.

INTERVENTIONS

The order of five cervical testing specimens was randomized for (1) ligase chain reaction (LCR) and (2) polymerase chain reaction (PCR) for both CT and GC; (3) transcription-mediated amplification (TMA) for CT; (4) culture for CT; and (5) cytology and LCR for GC and CT performed on ThinPrep Pap specimens. For CT and GC, a reference standard was based on three different tests performed on separate specimens. Generalized estimating equations were used to account for repeated measures.

MAIN OUTCOME MEASURE

Sensitivity and specificity of diagnostic tests.

RESULTS

The proportion of inadequate Pap smears was independent of specimen order. As a group, nucleic acid amplification test (NAAT) sensitivity and specificity for GC and CT were similar in the first two (early) and last three (late) swabs. Although point estimates for sensitivity were higher in the early swabs compared to the late swabs for GC LCR (13% difference), GC PCR (13%), and CT TMA (10%), these differences were not statistically significant. Their clinical significance warrants further investigation.

CONCLUSIONS

In clinical settings where both Pap smears and STI testing are performed in adolescents, clinical considerations can influence the order of specimen collection, since neither Pap specimen adequacy nor test performance of NAAT for CT and GC were significantly associated with swab order.

Human DNA polymerase iota incorporates dCTP opposite template G via a G.C + Hoogsteen base pair

Human DNA polymerase iota (hPoliota), a member of the Y family of DNA polymerases, differs in remarkable ways from other DNA polymerases, incorporating correct nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines. We present here the crystal structure of hPoliota bound to template G and incoming dCTP, which reveals a G.C + Hoogsteen base pair in a DNA polymerase active site. We show that the hPoliota active site has evolved to favor Hoogsteen base pairing, wherein the template sugar is fixed in a cavity that reduces the C1'-C1' distance across the nascent base pair from approximately 10.5 A in other DNA polymerases to 8.6 A in hPoliota. The rotation of G from anti to syn is then largely in response to this curtailed C1'-C1' distance. A G.C+ Hoogsteen base pair suggests a specific mechanism for hPoliota's ability to bypass N(2)-adducted guanines that obstruct replication.

Yeast and human translesion DNA synthesis polymerases: expression, purification, and biochemical characterization

The emergence of translesion DNA synthesis (TLS) as a primary mechanism by which eukaryotic cells tolerate DNA damage has led to a large effort to characterize the biochemical properties of the individual DNA polymerases and their roles in promoting replication past DNA lesions. The low-fidelity Y family DNA polymerases constitute a large proportion of TLS polymerases, and four of the five subfamilies of this class of polymerases are represented in eukaryotes. The eukaryotic B family DNA polymerase Polzeta also functions in TLS. We have had success in expressing and purifying these TLS polymerases from yeast cells, sometimes in milligram quantities. The purified proteins have been used to determine their ability to synthesize DNA on various modified templates and to analyze the kinetic efficiencies with which bypass occurs. Purified proteins have also been used to determine the X-ray crystal structures of several Y-family DNA polymerases. This chapter describes a general outline of methods used in our laboratory for the expression and purification of these TLS DNA polymerases from yeast cells and for assaying some of their biochemical properties.

Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain

The Rev1 protein of Saccharomyces cerevisiae functions in translesion synthesis (TLS) together with DNA polymerase (Pol) zeta, which is comprised of the Rev3 catalytic and the Rev7 accessory subunits. Rev1, a member of the Y family of Pols, differs from other members in its high degree of specificity for incorporating a C opposite template G as well as opposite an abasic site. Although Rev1 is indispensable for Polzeta-dependent TLS, its DNA synthetic activity is not required for many of the Polzeta-dependent lesion bypass events. This observation has suggested a structural role for Rev1 in this process. Here we show that in yeast, Rev1 forms a stable complex with Rev7, and the two proteins copurify. Importantly, the polymerase-associated domain (PAD) of Rev1 mediates its binding to Rev7. These observations reveal a novel role for the PAD region of Rev1 in protein-protein interactions, and they raise the possibility of a similar involvement of the PAD of other Y family Pols in protein-protein interactions. We discuss the possible roles of Rev1 versus the Rev1-Rev7 complex in TLS.