DNA polymerase ε leading strand signature mutations result from defects in its proofreading activity

The evidence that purified pol2-M644G DNA polymerase (Pol)ε exhibits a highly elevated bias for forming T:dTTP mispairs over A:dATP mispairs and that yeast cells harboring this Polε mutation accumulate A > T signature mutations in the leading strand have been used to assign a role for Polε in replicating the leading strand. Here, we determine whether A > T signature mutations result from defects in Polε proofreading activity by analyzing their rate in Polε proofreading defective pol2-4 and pol2-M644G cells. Since purified pol2-4 Polε exhibits no bias for T:dTTP mispair formation, A > T mutations are expected to occur at a much lower rate in pol2-4 than in pol2-M644G cells if Polε replicated the leading strand. Instead, we find that the rate of A > T signature mutations are as highly elevated in pol2-4 cells as in pol2-M644G cells; furthermore, the highly elevated rate of A > T signature mutations is severely curtailed in the absence of PCNA ubiquitination or Polζ in both the pol2-M644G and pol2-4 strains. Altogether, our evidence supports the conclusion that the leading strand A > T signature mutations derive from defects in Polε proofreading activity and not from the role of Polε as a leading strand replicase, and it conforms with the genetic evidence for a major role of Polδ in replication of both the DNA strands.

Mismatch repair operates at the replication fork in direct competition with mismatch extension by DNA polymerase δ

DNA mismatch repair (MMR) in eukaryotes is believed to occur post-replicatively, wherein nicks or gaps in the nascent DNA strand are suggested to serve as strand discrimination signals. However, how such signals are generated in the nascent leading strand has remained unclear. Here we examine the alternative possibility that MMR occurs in conjunction with the replication fork. To this end, we utilize mutations in the PCNA interacting peptide (PIP) domain of the Pol3 or Pol32 subunit of DNA polymerase δ (Polδ) and show that these pip mutations suppress the greatly elevated mutagenesis in yeast strains harboring the pol3-01 mutation defective in Polδ proofreading activity. And strikingly, they suppress the synthetic lethality of pol3-01 pol2-4 double mutant strains, which arises from the vastly enhanced mutability due to defects in the proofreading functions of both Polδ and Polε. Our finding that suppression of elevated mutagenesis in pol3-01 by the Polδ pip mutations requires intact MMR supports the conclusion that MMR operates at the replication fork in direct competition with other mismatch removal processes and with extension of synthesis from the mispair by Polδ. Furthermore, the evidence that Polδ pip mutations eliminate almost all the mutability of pol2-4 msh2Δ or pol3-01 pol2-4 adds strong support for a major role of Polδ in replication of both the leading and lagging DNA strands.

Inner southern magnetosphere observation of Mercury via SERENA ion sensors in BepiColombo mission

Mercury's southern inner magnetosphere is an unexplored region as it was not observed by earlier space missions. In October 2021, BepiColombo mission has passed through this region during its first Mercury flyby. Here, we describe the observations of SERENA ion sensors nearby and inside Mercury's magnetosphere. An intermittent high-energy signal, possibly due to an interplanetary magnetic flux rope, has been observed downstream Mercury, together with low energy solar wind. Low energy ions, possibly due to satellite outgassing, were detected outside the magnetosphere. The dayside magnetopause and bow-shock crossing were much closer to the planet than expected, signature of a highly eroded magnetosphere. Different ion populations have been observed inside the magnetosphere, like low latitude boundary layer at magnetopause inbound and partial ring current at dawn close to the planet. These observations are important for understanding the weak magnetosphere behavior so close to the Sun, revealing details never reached before.

Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase

PrimPol is a human DNA polymerase-primase that localizes to mitochondria and nucleus and bypasses the major oxidative lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis, in mostly error-free manner. We present structures of PrimPol insertion complexes with a DNA template-primer and correct dCTP or erroneous dATP opposite the lesion, as well as extension complexes with C or A as a 3′−terminal primer base. We show that during the insertion of C and extension from it, the active site is unperturbed, reflecting the readiness of PrimPol to accommodate oxoG(anti). The misinsertion of A opposite oxoG(syn) also does not alter the active site, and is likely less favorable due to lower thermodynamic stability of the oxoG(syn)•A base-pair. During the extension step, oxoG(syn) induces an opening of its base-pair with A or misalignment of the 3′-A primer terminus. Together, the structures show how PrimPol accurately synthesizes DNA opposite oxidatively damaged DNA in human cells.

The human DNA primase and DNA polymerase PrimPol replicates through the major oxidative DNA damage lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis in a mostly error-free manner thus suppressing oxoG-induced mutagenesis in mitochondria and the nucleus. Here, the authors present crystal structures of PrimPol in complex with an oxoG lesion in different contexts that provide mechanistic insights into how PrimPol performs predominantly accurate synthesis on oxidative-damaged DNAs in human cells.

A novel role of DNA polymerase λ in translesion synthesis in conjunction with DNA polymerase ζ

As an integral scaffolding component of DNA polymerase (Pol) zeta, Pol lambda adapts Pol zeta–dependent translesion synthesis to operate in a predominantly error-free manner in human cells.

By extending synthesis opposite from a diverse array of DNA lesions, DNA polymerase (Pol) ζ performs a crucial role in translesion synthesis (TLS). In yeast and cancer cells, Rev1 functions as an indispensable scaffolding component of Polζ and it imposes highly error-prone TLS upon Polζ. However, for TLS that occurs during replication in normal human cells, Rev1 functions instead as a scaffolding component of Pols η, ι, and κ and Rev1-dependent TLS by these Pols operates in a predominantly error-free manner. The lack of Rev1 requirement for Polζ function in TLS in normal cells suggested that some other protein substitutes for this Rev1 role. Here, we identify a novel role of Polλ as an indispensable scaffolding component of Polζ. TLS studies opposite a number of DNA lesions support the conclusion that as an integral component, Polλ adapts Polζ-dependent TLS to operate in a predominantly error-free manner in human cells, essential for genome integrity and cellular homeostasis.

SERENA: Particle Instrument Suite for Determining the Sun-Mercury Interaction from BepiColombo

The ESA-JAXA BepiColombo mission to Mercury will provide simultaneous measurements from two spacecraft, offering an unprecedented opportunity to investigate magnetospheric and exospheric particle dynamics at Mercury as well as their interactions with solar wind, solar radiation, and interplanetary dust. The particle instrument suite SERENA (Search for Exospheric Refilling and Emitted Natural Abundances) is flying in space on-board the BepiColombo Mercury Planetary Orbiter (MPO) and is the only instrument for ion and neutral particle detection aboard the MPO. It comprises four independent sensors: ELENA for neutral particle flow detection, Strofio for neutral gas detection, PICAM for planetary ions observations, and MIPA, mostly for solar wind ion measurements. SERENA is managed by a System Control Unit located inside the ELENA box. In the present paper the scientific goals of this suite are described, and then the four units are detailed, as well as their major features and calibration results. Finally, the SERENA operational activities are shown during the orbital path around Mercury, with also some reference to the activities planned during the long cruise phase.

Genetic evidence for reconfiguration of DNA polymerase θ active site for error-free translesion synthesis in human cells

The action mechanisms revealed by the biochemical and structural analyses of replicative and translesion synthesis (TLS) DNA polymerases (Pols) are retained in their cellular roles. In this regard, DNA polymerase θ differs from other Pols in that whereas purified Polθ misincorporates an A opposite 1,N6-ethenodeoxyadenosine (ϵdA) using an abasic-like mode, Polθ performs predominantly error-free TLS in human cells. To test the hypothesis that Polθ adopts a different mechanism for replicating through ϵdA in human cells than in the purified Pol, here we analyze the effects of mutations in the two highly conserved tyrosine residues, Tyr-2387 and Tyr-2391, in the Polθ active site. Our findings that these residues are indispensable for TLS by the purified Pol but are not required in human cells, as well as other findings, provide strong evidence that the Polθ active site is reconfigured in human cells to stabilize ϵdA in the syn conformation for Hoogsteen base pairing with the correct nucleotide. The evidence that a DNA polymerase can configure its active site entirely differently in human cells than in the purified Pol establishes a new paradigm for DNA polymerase function.

Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme

DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.

DNA polymerase θ accomplishes translesion synthesis opposite 1,N6-ethenodeoxyadenosine with a remarkably high fidelity in human cells

Here we show that translesion synthesis (TLS) opposite 1,N6-ethenodeoxyadenosine (εdA), which disrupts Watson-Crick base pairing, occurs via Polι/Polζ-, Rev1-, and Polθ-dependent pathways. The requirement of Polι/Polζ is consistent with the ability of Polι to incorporate nucleotide opposite εdA by Hoogsteen base pairing and of Polζ to extend synthesis. Rev1 polymerase and Polθ conduct TLS opposite εdA via alternative error-prone pathways. Strikingly, in contrast to extremely error-prone TLS opposite εdA by purified Polθ, it performs predominantly error-free TLS in human cells. Reconfiguration of the active site opposite εdA would provide Polθ the proficiency for error-free TLS in human cells.

Population-attributable fraction of tubal factor infertility associated with chlamydia

BACKGROUND

Chlamydia trachomatis infection is highly prevalent among young women in the United States. Prevention of long-term sequelae of infection, including tubal factor infertility, is a primary goal of chlamydia screening and treatment activities. However, the population-attributable fraction of tubal factor infertility associated with chlamydia is unclear, and optimal measures for assessing tubal factor infertility and prior chlamydia in epidemiological studies have not been established. Black women have increased rates of chlamydia and tubal factor infertility compared with White women but have been underrepresented in prior studies of the association of chlamydia and tubal factor infertility.

OBJECTIVES

The objectives of the study were to estimate the population-attributable fraction of tubal factor infertility associated with Chlamydia trachomatis infection by race (Black, non-Black) and assess how different definitions of Chlamydia trachomatis seropositivity and tubal factor infertility affect population-attributable fraction estimates.

STUDY DESIGN

We conducted a case-control study, enrolling infertile women attending infertility practices in Birmingham, AL, and Pittsburgh, PA, during October 2012 through June 2015. Tubal factor infertility case status was primarily defined by unilateral or bilateral fallopian tube occlusion (cases) or bilateral fallopian tube patency (controls) on hysterosalpingogram. Alternate tubal factor infertility definitions incorporated history suggestive of tubal damage or were based on laparoscopic evidence of tubal damage. We aimed to enroll all eligible women, with an expected ratio of 1 and 3 controls per case for Black and non-Black women, respectively. We assessed Chlamydia trachomatis seropositivity with a commercial assay and a more sensitive research assay; our primary measure of seropositivity was defined as positivity on either assay. We estimated Chlamydia trachomatis seropositivity and calculated Chlamydia trachomatis-tubal factor infertility odds ratios and population-attributable fraction, stratified by race.

RESULTS

We enrolled 107 Black women (47 cases, 60 controls) and 620 non-Black women (140 cases, 480 controls). Chlamydia trachomatis seropositivity by either assay was 81% (95% confidence interval, 73-89%) among Black and 31% (95% confidence interval, 28-35%) among non-Black participants (P < .001). Using the primary Chlamydia trachomatis seropositivity and tubal factor infertility definitions, no significant association was detected between chlamydia and tubal factor infertility among Blacks (odds ratio, 1.22, 95% confidence interval, 0.45-3.28) or non-Blacks (odds ratio, 1.41, 95% confidence interval, 0.95-2.09), and the estimated population-attributable fraction was 15% (95% confidence interval, -97% to 68%) among Blacks and 11% (95% confidence interval, -3% to 23%) among non-Blacks. Use of alternate serological measures and tubal factor infertility definitions had an impact on the magnitude of the chlamydia-tubal factor infertility association and resulted in a significant association among non-Blacks.

CONCLUSION

Low population-attributable fraction estimates suggest factors in addition to chlamydia contribute to tubal factor infertility in the study population. However, high background Chlamydia trachomatis seropositivity among controls, most striking among Black participants, could have obscured an association with tubal factor infertility and resulted in a population-attributable fraction that underestimates the true etiological role of chlamydia. Choice of chlamydia and tubal factor infertility definitions also has an impact on the odds ratio and population-attributable fraction estimates.

Most American Association of Oral and Maxillofacial Surgeons Members Have Not Adopted the American Society of Anesthesiologists-Recommended Nil Per Os Guidelines

PURPOSE

The purpose of this study was to determine if American Association of Oral and Maxillofacial Surgeons members have integrated the current American Society of Anesthesiologists (ASA) nil per os (NPO) guidelines into their preoperative instructions.

MATERIALS AND METHODS

We designed and implemented a cross-sectional study and enrolled a random sample of private-practice American Association of Oral and Maxillofacial Surgeons members who practice in the United States. The predictor variables were year of graduation from residency, dual degree (MD and DDS or DMD) or single degree, and region. The primary outcome variable was adoption of the ASA NPO guidelines, defined as recommending fasting times of 2 hours for clear liquids and 6 hours for solid foods. To collect data, a systematic online search was implemented. Appropriate univariate and bivariate statistics were computed, and the level of significance was set at .05; in addition, 95% confidence intervals were calculated.

RESULTS

The study sample was composed of 431 oral and maxillofacial surgeons (OMSs). Almost all of the study sample (99.1%) did not adopt the ASA guidelines. The fasting recommendations were different from 2 hours for clear liquids and 6 hours for solid foods. However, recommendations of 2 hours or greater for clear liquids were made by 99.8% of OMSs, and recommendations of 6 hours or greater for solid foods were made by 99.3%. Only 4.4% of OMSs made different recommendations for clear liquids and solid foods. No substantial association was found between whether OMSs adopted the most current ASA guidelines and the year they graduated from residency or the obtainment of dual degrees.

CONCLUSIONS

OMSs in private practice are overwhelmingly recommending longer fasting times for clear liquids and solid foods on their Web sites when compared with the current ASA guidelines before ambulatory anesthesia. The ASA guidelines are based on meta-analysis; therefore, deviations in practice, although not incorrect, may call for discussion.

Effectiveness of neuromuscular electrical stimulation for management of shoulder subluxation post-stroke: a systematic review with meta-analysis

Objectives:

To examine the effectiveness of neuromuscular electrical stimulation (NMES) for the management of shoulder subluxation after stroke including assessment of short (1 hour or less) and long (more than one hour) daily treatment duration.

Data sources:

MEDLINE, CENTRAL, CINAHL, WOS, KoreaMed, RISS and reference lists from inception to January 2017

Review methods:

We considered randomized controlled trials that reported neuromuscular electrical stimulation for the treatment of shoulder subluxation post-stroke. Two reviewers independently selected trials for inclusion, assessed trial quality, and extracted data.

Results:

Eleven studies were included (432 participants); seven studies were good quality, four were fair. There was a significant treatment effect of neuromuscular electrical stimulation for reduction of subluxation for persons with acute and subacute stroke (SMD:–1.11; 95% CI:–1.53, –0.68) with either short (SMD:–0.91; 95% CI:–1.43, –0.40) or long (SMD:–1.49; 95% CI:–2.31, –0.67) daily treatment duration. The effect for patients with chronic stroke was not significant (SMD:–1.25; 95% CI:–2.60, 0.11). There was no significant effect of neuromuscular electrical stimulation on arm function or shoulder pain.

Conclusion:

This meta-analysis suggests a beneficial effect of neuromuscular electrical stimulation, with either short or long daily treatment duration, for reducing shoulder subluxation in persons with acute and subacute stroke. No significant benefits were observed for persons with chronic stroke or for improving arm function or reducing shoulder pain.

Structure and mechanism of human PrimPol, a DNA polymerase with primase activity

PrimPol is a novel human enzyme that contains both DNA primase and DNA polymerase activities. We present the first structure of human PrimPol in ternary complex with a DNA template-primer and an incoming deoxynucleoside triphosphate (dNTP). The ability of PrimPol to function as a DNA primase stems from a simple but remarkable feature-almost complete lack of contacts to the DNA primer strand. This, in turn, allows two dNTPs to bind initiation and elongation sites on the enzyme for the formation of the first dinucleotide. PrimPol shows the ability to synthesize DNA opposite ultraviolet (UV) lesions; however, unexpectedly, the active-site cleft of the enzyme is constrained, which precludes the bypass of UV-induced DNA lesions by conventional translesion synthesis. Together, the structure addresses long-standing questions about how DNA primases actually initiate synthesis and how primase and polymerase activities combine in a single enzyme to carry out DNA synthesis.

Human DNA polymerase α in binary complex with a DNA:DNA template-primer

The Polα/primase complex assembles the short RNA-DNA fragments for priming of lagging and leading strand DNA replication in eukaryotes. As such, the Polα polymerase subunit encounters two types of substrates during primer synthesis: an RNA:DNA helix and a DNA:DNA helix. The engagement of the polymerase subunit with the DNA:DNA helix has been suggested as the of basis for primer termination in eukaryotes. However, there is no structural information on how the Polα polymerase subunit actually engages with a DNA:DNA helix during primer synthesis. We present here the first crystal structure of human Polα polymerase subunit in complex with a DNA:DNA helix. Unexpectedly, we find that portion of the DNA:DNA helix in contact with the polymerase is not in a B-form but in a hybrid A-B form. Almost all of the contacts observed previously with an RNA primer are preserved with a DNA primer – with the same set of polymerase residues tracking the sugar-phosphate backbone of the DNA or RNA primer. Thus, rather than loss of specific contacts, the free energy cost of distorting DNA from B- to hybrid A-B form may augur the termination of primer synthesis in eukaryotes.

A Major Role of DNA Polymerase δ in Replication of Both the Leading and Lagging DNA Strands

Genetic studies with S. cerevisiae Polδ (pol3-L612M) and Polε (pol2-M644G) mutant alleles, each of which display a higher rate for the generation of a specific mismatch, have led to the conclusion that Polε is the primary leading strand replicase and that Polδ is restricted to replicating the lagging strand template. Contrary to this widely accepted view, here we show that Polδ plays a major role in the replication of both DNA strands, and that the paucity of pol3-L612M-generated errors on the leading strand results from their more proficient removal. Thus, the apparent lack of Polδ contribution to leading strand replication is due to differential mismatch removal rather than differential mismatch generation. Altogether, our genetic studies with Pol3 and Pol2 mutator alleles support the conclusion that Polδ, and not Polε, is the major DNA polymerase for carrying out both leading and lagging DNA synthesis.

Retrograde plasticity and differential competition of bipolar cell dendrites and axons in the developing retina

Most neurons function in the context of pathways that process and propagate information through a series of stages, e.g., from the sensory periphery to cerebral cortex. Because activity at each stage of a neural pathway depends on connectivity at the preceding one, we hypothesized that during development, axonal output of a neuron may regulate synaptic development of its dendrites (i.e., retrograde plasticity). Within pathways, neurons often receive input from multiple partners and provide output to targets shared with other neurons (i.e., convergence). Converging axons can intermingle or occupy separate territories on target dendrites. Activity-dependent competition has been shown to bias target innervation by overlapping axons in several systems. By contrast, whether territorial axons or dendrites compete for targets and inputs, respectively, has not been tested. Here, we generate transgenic mice in which glutamate release from specific sets of retinal bipolar cells (BCs) is suppressed. We find that dendrites of silenced BCs recruit fewer inputs when their neighbors are active and that dendrites of active BCs recruit more inputs when their neighbors are silenced than either active or silenced BCs with equal neighbors. By contrast, axons of silenced BCs form fewer synapses with their targets, irrespective of the activity of their neighbors. These findings reveal that retrograde plasticity guides BC dendritic development in vivo and demonstrate that dendrites, but not territorial axons, in a convergent neural pathway engage in activity-dependent competition. We propose that at a population level, retrograde plasticity serves to maximize functional representation of inputs.

Crystal structure of yeast DNA polymerase ε catalytic domain

DNA polymerase ε (Polε) is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Here we report the ternary structure of the Polε catalytic subunit (Pol2) bound to a nascent G:C base pair (Pol2G:C). Pol2G:C has a typical B-family polymerase fold and embraces the template-primer duplex with the palm, fingers, thumb and exonuclease domains. The overall arrangement of domains is similar to the structure of Pol2T:A reported recently, but there are notable differences in their polymerase and exonuclease active sites. In particular, we observe Ca2+ ions at both positions A and B in the polymerase active site and also observe a Ca2+ at position B of the exonuclease site. We find that the contacts to the nascent G:C base pair in the Pol2G:C structure are maintained in the Pol2T:A structure and reflect the comparable fidelity of Pol2 for nascent purine-pyrimidine and pyrimidine-purine base pairs. We note that unlike that of Pol3, the shape of the nascent base pair binding pocket in Pol2 is modulated from the major grove side by the presence of Tyr431. Together with Pol2T:A, our results provide a framework for understanding the structural basis of high fidelity DNA synthesis by Pol2.

An iron-sulfur cluster in the polymerase domain of yeast DNA polymerase ε

DNA polymerase ε (Polε) is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Polε from Saccharomyces cerevisiae is composed of four subunits--Pol2, Dpb2, Dpb3, and Dpb4. Here, we report the presence of a [Fe-S] cluster directly within the active polymerase domain of Pol2 (residues 1-1187). We show that binding of the [Fe-S] cluster is mediated by cysteines in an insertion (Pol2(ins)) that is conserved in Pol2 orthologs but is absent in the polymerase domains of Polα, Polδ, and Polζ. We also show that the [Fe-S] cluster is required for Pol2 polymerase activity but not for its exonuclease activity. Collectively, our work suggests that Polε is perhaps more sensitive than other DNA polymerases to changes in oxidative stress in eukaryotic cells.

The architecture of yeast DNA polymerase ζ

DNA polymerase ζ (Polζ) is specialized for the extension step of translesion DNA synthesis (TLS). Despite its central role in maintaining genome integrity, little is known about its overall architecture. Initially identified as a heterodimer of the catalytic subunit Rev3 and the accessory subunit Rev7, yeast Polζ has recently been shown to form a stable four-subunit enzyme (Polζ-d) upon the incorporation of Pol31 and Pol32, the accessory subunits of yeast Polδ. To understand the 3D architecture and assembly of Polζ and Polζ-d, we employed electron microscopy. We show here how the catalytic and accessory subunits of Polζ and Polζ-d are organized relative to each other. In particular, we show that Polζ-d has a bilobal architecture resembling the replicative polymerases and that Pol32 lies in proximity to Rev7. Collectively, our study provides views of Polζ and Polζ-d and a structural framework for understanding their roles in DNA damage bypass.

Design effects for sample size computation in three-level designs

Experiments with multiple nested levels where randomization can take place at any level bring challenges to the computation of sample sizes. Formulas derived under simple single-level experiments must be adjusted using multiplicative factors or design effects. In this work, we take a unified approach to finding the design effects in terms of intracluster correlations and present formulas to compute sample sizes of different levels. Equal cluster sample sizes and homogeneous within cluster variances are assumed.

Interactive preventive health record to enhance delivery of recommended care: a randomized trial

PURPOSE

Americans receive only one-half of recommended preventive services. Information technologies have been advocated to engage patients. We tested the effectiveness of an interactive preventive health record (IPHR) that links patients to their clinician's record, explains information in lay language, displays tailored recommendations and educational resources, and generates reminders.

METHODS

This randomized controlled trial involved 8 primary care practices. Four thousand five hundred patients were randomly selected to receive a mailed invitation to use the IPHR or usual care. Outcomes were measured using patient surveys and electronic medical record data and included IPHR use and service delivery. Comparisons were made between invited and usual-care patients and between users and nonusers among those invited to use the IPHR.

RESULTS

At 4 and 16 months, 229 (10.2%) and 378 (16.8%) of invited patients used the IPHR. The proportion of patients up-to-date with all services increased between baseline and 16 months by 3.8% among intervention patients (from 11.4% to 15.2%, P <.001) and by 1.5% among control patients (from 11.1% to 12.6%, P = .07), a difference of 2.3% (P = .05). Greater increases were observed among patients who used the IPHR. At 16 months, 25.1% of users were up-to-date with all services, double the rate among nonusers. At 4 months, delivery of colorectal, breast, and cervical cancer screening increased by 19%, 15%, and 13%, respectively, among users.

CONCLUSIONS

Information systems that feature patient-centered functionality, such as the IPHR, have potential to increase preventive service delivery. Engaging more patients to use systems could have important public health benefits.

A novel ubiquitin binding mode in the S. cerevisiae translesion synthesis DNA polymerase η

The ubiquitin binding zinc finger (UBZ) domain in the C-terminal portion of Polη has been found to interact with ubiquitin. However, the affinity between the Polη UBZ and ubiquitin was shown to be low with a previously reported K(d) of 73-81 μM. This low-affinity binding between Polη UBZ and ubiquitin has been difficult to reconcile with its presumed role in translesion synthesis as suggested by genetic and cell biology studies. In this work, we constructed a minimal S. cerevisiae Polη UBZ domain and probed the Polη UBZ-ubiquitin interaction using a surface plasmon resonance (SPR) technique. Our quantitative binding data between the wild-type or mutant Polη UBZ and ubiquitin revealed an interesting divergence between the Polη UBZ from S. cerevisiae and humans. Moreover, we found that the C-terminal portion of yeast Polη (amino acid 515-632) binds ubiquitin with a much higher affinity than the minimal UBZ domain. Further, distinct ubiquitin-binding kinetics were observed for the C-terminal portion of Polη and the isolated UBZ domain. This observation raised the interesting possibility that the Polη C-terminal portion binds ubiquitin in a novel mode that affords higher affinity. Our findings have broader implication in understanding the generally weak interaction between the known ubiquitin-binding domains and ubiquitin.

Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase η

7,8-dihydro-8-oxoguanine (8-oxoG) adducts are formed frequently by the attack of oxygen-free radicals on DNA. They are among the most mutagenic lesions in cells because of their dual coding potential, where, in addition to normal base-pairing of 8-oxoG(anti) with dCTP, 8-oxoG in the syn conformation can base pair with dATP, causing G to T transversions. We provide here for the first time a structural basis for the error-free replication of 8-oxoG lesions by yeast DNA polymerase η (Polη). We show that the open active site cleft of Polη can accommodate an 8-oxoG lesion in the anti conformation with only minimal changes to the polymerase and the bound DNA: at both the insertion and post-insertion steps of lesion bypass. Importantly, the active site geometry remains the same as in the undamaged complex and provides a basis for the ability of Polη to prevent the mutagenic replication of 8-oxoG lesions in cells.

Commutability Limitations Influence Quality Control Results with Different Reagent Lots

BACKGROUND

Good laboratory practice includes verifying that each new lot of reagents is suitable for use before it is put into service. Noncommutability of quality control (QC) samples with clinical patient samples may preclude their use to verify consistency of results for patient samples between different reagent lots.

METHODS

Patient sample results and QC data were obtained from reagent lot change verification records for 18 QC materials, 661 reagent lot changes, 1483 reagent lot change–QC events, 82 analytes, and 7 instrument platforms. The significance of between-lot differences in the results for QC samples compared with those for patient samples was assessed by a modified 2-sample t test adjusted for heterogeneity of QC and patient sample measurement variances.

RESULTS

Overall, 40.9% of reagent lot change–QC events had a significant difference (P &lt; 0.05) between results for QC samples compared with results for patient samples between 2 reagent lots. For QC results with differences &lt;1.0 SD interval (83.1% of total), 37.7% were significantly different from the changes observed for patient samples. For QC results with differences ≥1.0 SD interval (16.9% of total), 57.0% were significantly different from those for patient samples.

CONCLUSIONS

Occurrence of noncommutable results for QC materials was frequent enough that the QC results could not be used to verify consistency of results for patient samples when changing lots of reagents.

DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase

Abasic (apurinic/apyrimidinic) sites are among the most abundant DNA lesions in humans, and they present a strong block to replication. They are also highly mutagenic because when replicative DNA polymerases manage to insert a nucleotide opposite the lesion, they prefer to insert an A. Rev1, a member of Y-family DNA polymerases, does not obey the A-rule. This enzyme inserts a C opposite an abasic lesion with much greater catalytic efficiency than an A, G, or T. We present here the structure of yeast Rev1 in ternary complex with DNA containing an abasic lesion and with dCTP as the incoming nucleotide. The structure reveals a mechanism of synthesis across an abasic lesion that differs from that in other polymerases. The lesion is driven to an extrahelical position, and the incorporation of a C is mediated by an arginine (Arg324) that is conserved in all known orthologs of Rev1, including humans. The hydrophobic cavity that normally accommodates the unmodified G is instead filled with water molecules. Since Gs are especially prone to depurination through a spontaneous hydrolysis of the glycosidic bond, the ability of Rev1 to stabilize an abasic lesion in its active site and employ a surrogate arginine to incorporate a C provides a unique means for the "error-free" bypass of this noninstructional lesion.

Characterizing the freeze-drying behavior of model protein formulations

The freeze-drying behavior of three model proteins, namely, lysozyme, BSA, and IgG, has been studied using a variety of techniques under two different primary drying conditions (shelf temperatures of -25°C and +25°C, respectively) in an amorphous formulation. Manometric temperature measurements were used to characterize product temperature (T (pr)), sublimation rates, and product resistance (R (p)) during primary drying. Biophysical techniques such as circular dichroism, fluorescence, and Fourier transform infrared spectroscopy were used to study protein conformation. Size exclusion chromatography was used to monitor the formation of high-molecular-weight species (HMWS) over time on storage, and cake morphology was studied using scanning electron microscopy. The differences in the freeze-drying behavior of the three proteins were more evident at higher protein concentrations, where the protein significantly influences the behavior of the formulation matrix. However, these differences were minimized in the aggressive mode and were insignificant at lower protein concentrations where excipients dominated the freeze-drying behavior. Differences in cake morphology were observed between the two drying conditions employed as well as between the three proteins studied. The stability and the protein structure, however, were equivalent for the protein cakes generated using the two different primary drying conditions.

Pre-steady state kinetic studies of the fidelity of nucleotide incorporation by yeast DNA polymerase delta

Eukaryotic DNA polymerase delta (pol delta) is a member of the B family of polymerases and synthesizes most of the lagging strand during DNA replication. Yeast pol delta is a heterotrimer comprised of three subunits: the catalytic subunit (Pol3) and two accessory subunits (Pol31 and Pol32). Although pol delta is one of the major eukaryotic replicative polymerase, the mechanism by which it incorporates nucleotides is unknown. Here we report both steady state and pre-steady state kinetic studies of the fidelity of pol delta. We found that pol delta incorporates nucleotides with an error frequency of 10(-4) to 10(-5). Furthermore, we showed that for correct versus incorrect nucleotide incorporation, there are significant differences between both pre-steady state kinetic parameters (apparent K(d)(dNTP) and k(pol)). Somewhat surprisingly, we found that pol delta synthesizes DNA at a slow rate with a k(pol) of approximately 1 s(-1). We suggest that, unlike its prokaryotic counterparts, pol delta requires replication accessory factors like proliferating cell nuclear antigen to achieve rapid rates of nucleotide incorporation.

ANAEROBIC GLYCOGENOLYSIS IN THE MUSCLES OF RANA PIPIENS LIVING AT LOW TEMPERATURES

1. A considerable proportion of R. pipiens caught in the spring and stored without food for several weeks at about 4 degrees C. had gastrocnemii that did not break down glycogen when they contracted anaerobically to complete exhaustion. A smaller number of the same muscles did not produce lactate. 2. There was no evident relation between failure to break down glycogen and the glycogen content of such muscles, some of which had more than 500 mg. of glycogen per 100 gm. of tissue. 3. The hypothesis of Meyerhof and his followers that aerobic contraction of frog muscles may at times take place with sources of energy other than carbohydrate is therefore extended to include anaerobic contraction.

Protective immunity to Chlamydia trachomatis genital infection: evidence from human studies

Background. Some screening and treatment programs implemented to control Chlamydia trachomatis genital infections and their complications have shown initial reductions in infection prevalence, followed by increases to preprogram levels or higher. One hypothesis is that treatment shortens duration of infection, attenuates development of protective immunity, and thereby, increases risk of reinfection. Methods. A literature review was undertaken to assess evidence supporting the concept of protective immunity,its characteristics, and its laboratory correlates in human chlamydial infection. The discussion is organized around key questions formulated in preparation for the Chlamydia Immunology and Control Expert Advisory Meeting held by the Centers for Disease Control and Prevention in April 2008. Results. Definitive human studies are not available, but cross-sectional studies show that chlamydia prevalence,organism load, and concordance rates in couples decrease with age, and organism load is lower in those with repeat infections, supporting the concept of protective immunity. The protection appears partial and can be overcome after reexposure, similar to what has been found in rodent models of genital infection. No data are available to define the duration of infection required to confer a degree of immunity or the time course of immunity after resolution of untreated infection. In longitudinal studies involving African sex workers, a group presumed to have frequent and ongoing exposure to chlamydial infection, interferon-g production by peripheral blood mononuclear cells in response to chlamydial heat-shock protein 60 was associated with low risk of incident infection.In cross-sectional studies, relevant T helper 1-type responses were found in infected persons, paralleling the studies in animal models. Conclusions. The data support the concept that some degree of protective immunity against reinfection develops after human genital infection, although it appears, at best, to be partial. It is likely that factors besides population levels of immunity contribute to trends in prevalence observed in screening and treatment programs.Future studies of protective immunity in humans will require longitudinal follow-up of individuals and populations,frequent biological and behavioral sampling, and special cohorts to help control for exposure.

Patient weight counseling choices and outcomes following a primary care and community collaborative intervention

OBJECTIVE

Obesity has become a public health epidemic in adults and children. Clinician practices need new models to effectively address overweight in patients, yet, practices lack time and resources. We tested a clinician-delivered intervention that utilized community resources for in-depth counseling for unhealthy behaviors including overweight.

METHODS

Eligible patients in nine primary care practices were identified using an electronic linkage system (eLinkS) which also automated patient referrals to group (Weight Watcher's), telephone counseling (TC), or usual care. Pre/post-survey data were used to assess factors related to counseling choices as well as changes in BMI (kg/m(2)) and weight-related behaviors using descriptive statistics, unadjusted, and adjusted statistical analyses.

RESULTS

Study sample (n=146) was 70% female with a mean age of 57 years. More patients (57%) selected WW, followed by usual care (27%) or TC (16%). Age, gender, clinician recommendation, and counseling program characteristics were influential in counseling selections. Weight Watcher's participants and those in TC, reported statistically significant weight loss, WW participants also reported significant increases in fruit/vegetable intake; after 4 months compared with usual care.

CONCLUSIONS

This practice-based intervention utilizing community counseling referrals was associated with positive health behavior change.

PRACTICE IMPLICATIONS

Identifying influential factors related to patient weight counseling choices may help guide referrals to community programs.

The relative importance of patient-reported barriers to colorectal cancer screening

BACKGROUND

Colorectal cancer (CRC) screening rates are suboptimal. The most important barriers identified by patients are poorly understood. A comprehensive assessment of barriers to all recommended modalities is needed.

METHODS

In 2007, a questionnaire was mailed to 6100 patients, aged 50-75 years, from 12 family medicine practices in the Virginia Ambulatory Care Outcomes Research Network. People aged 65-75 years and African Americans were oversampled. Patients were asked to rate 19-21 barriers to each of four recommended tests. In 2008, responses were coded on a 5-point scale; higher scores reflected stronger barrier endorsement.

RESULTS

The response rate was 55% (n=3357). Approximately 40% of respondents were aged >/=65 years, 30% were African-American, and 73% were adherent to screening. A clinician's failure to suggest screening and not knowing testing was necessary received the highest mean scores as barriers. Financial concerns and misconceptions were also cited. Barrier scores differed depending on whether respondents were never screened, overdue for screening, or adherent to guidelines. The top five barriers for each modality included test-specific barriers (e.g., handling stool, bowel preparation), which often outranked generic barriers to screening. Not knowing testing was necessary was a top barrier for all tests but colonoscopy.

CONCLUSIONS

Although physician advice and awareness of the need for screening are important, barriers to screening are not homogenous across tests, and test-specific barriers warrant consideration in designing strategies to improve screening rates. Barrier scores differ by screening status, highlighting the need to address prior screening experience. Evidence that patients are more familiar with colonoscopy than with other modalities suggests an opportunity to improve screening rates by educating patients about alternative tests.

Promoting primary care smoking-cessation support with quitlines: the QuitLink Randomized Controlled Trial

BACKGROUND

Counseling by clinicians promotes smoking cessation, but in most U.S. primary care practices, it is difficult to provide more than brief advice to quit in the course of routine work. Telephone quitlines can deliver effective intensive counseling, but few collaborate closely with clinicians.

PURPOSE

This study aimed to determine whether cessation support in practices is enhanced by a systems approach, in partnership with quitlines.

DESIGN

A cluster RCT was used.

SETTING/PARTICIPANTS

Participants included 1817 adult smokers from 16 primary care practices in the Virginia Ambulatory Care Outcomes Research Network.

INTERVENTION

An expanded tobacco-use "vital sign" intervention (identify smokers, advise cessation, and assess readiness to quit) that was combined with fax referral of preparation-stage smokers to a quitline providing feedback to practices was compared to a traditional tobacco-use vital sign alone.

MAIN OUTCOME MEASURES

The frequency of cessation support (in-office discussion of methods to quit or quitline referral) reported by patients in an exit survey (September 2005-July 2006, analyzed in 2008) was measured.

RESULTS

The adjusted percentage of smokers who reported receiving cessation support differed by 12.5% in intervention and control practices (40.7% vs 28.2%, respectively; p<0.001). Both in-office discussion of methods to quit and quitline referral increased significantly with the intervention. Post hoc analysis revealed that the increase in cessation was stable for both patient gender and visit type and was more pronounced with patients aged 35-54 years and with male and more experienced clinicians.

CONCLUSIONS

A systems approach to identifying smokers, advising and assessing readiness to quit, combined with a partnership with a quitline, increases delivery of cessation support for primary care patients beyond that accomplished by traditional tobacco-use vital sign screening alone.

CLINICAL TRIAL REGISTRATION

NCT00112268.

Patient costs as a barrier to intensive health behavior counseling

BACKGROUND

Although intensive health behavior counseling has been demonstrated to help patients lose weight and quit smoking, many payers offer limited coverage for such counseling.

PURPOSE

This mixed-methods case study examined how coverage affected utilization of an electronic linkage system (eLinkS) to help adult patients obtain intensive health behavior counseling, provided through a collaboration of primary care practices and community programs.

METHODS

Grant support enabled patients to obtain counseling at no cost, but funds were exhausted within 5 weeks as a result of an overwhelming response. To study the influence of cost as a barrier, referrals were resumed for an additional 3 weeks, but patients were required to pay for them. Use of eLinkS, level of clinician counseling and referrals, and patient interest in referrals were measured using electronic medical record data and patient and clinician interviews.

RESULTS

When counseling was free, approximately one in five patients with an unhealthy behavior and an eLinkS prompt was referred for intensive counseling. However, when patient charges were instituted, referrals decreased by 97% (from 21.8% to 0.7%, p<0.001); clinicians asked fewer patients about health behaviors (37% vs 29%, p<0.001); clinicians offered fewer patients referrals (29% vs 6%, p<0.001); and patients were less interested in accepting referrals (76% vs 14%, p<0.001). In interviews, patients and clinicians cited cost as a major barrier.

CONCLUSIONS

Coverage for intensive health behavior counseling is important to utilization, particularly for interventions that involve clinician-community partnerships. The potential public health benefits of such collaborations to reduce unhealthy behaviors justify the elimination of financial barriers (e.g., copayments) by payers.

Avertable deaths associated with household income in Virginia

OBJECTIVES

We estimated how many deaths would be averted if the entire population of Virginia experienced the mortality rates of the 5 most affluent counties or cities.

METHODS

Using census data and vital statistics for the years 1990 through 2006, we applied the mortality rates of the 5 counties/cities with the highest median household income to the populations of all counties and cities in the state.

RESULTS

If the mortality rates of the reference population had applied to the entire state, 24.3% of deaths in Virginia from 1990 through 2006 (range = 21.8%-28.1%) would not have occurred. An annual mean of 12 954 deaths would have been averted (range = 10 548-14 569), totaling 220 211 deaths from 1990 through 2006. In some of the most disadvantaged areas of the state, nearly half of deaths would have been averted.

CONCLUSIONS

Favorable conditions that exist in areas with high household incomes exert a major influence on mortality rates. The corollary-that health suffers when society is exposed to economic stresses-is especially timely amid the current recession. Further research must clarify the extent to which individual-level factors (e.g., earnings, education, race, health insurance) and community characteristics can improve health outcomes.

Replication across template T/U by human DNA polymerase-iota

Human DNA polymerase-iota (Poliota) incorporates correct nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines. In fact, the fidelity opposite template T is so poor that Poliota inserts an incorrect dGTP approximately 10 times better than it inserts the correct dATP. We determine here how a template T/U is accommodated in the Poliota active site and why a G is incorporated more efficiently than an A. We show that in the absence of incoming dATP or dGTP (binary complex), template T/U exists in both syn and anti conformations, but in the presence of dATP or dGTP (ternary complexes), template T/U is predominantly in the anti conformation. We also show that dATP and dGTP insert differently opposite template T/U, and that the basis of selection of dGTP over dATP is a hydrogen bond between the N2 amino group of dGTP and Gln59 of Poliota.