Human DNA polymerase iota promotes replication through a ring-closed minor-groove adduct that adopts a syn conformation in DNA

Acrolein, an alpha,beta-unsaturated aldehyde, is generated in vivo as the end product of lipid peroxidation and from oxidation of polyamines. The reaction of acrolein with the N2 group of guanine in DNA leads to the formation of a cyclic adduct, gamma-hydroxy-1,N2-propano-2'-deoxyguanosine (gamma-HOPdG). Previously, we have shown that proficient replication through the gamma-HOPdG adduct can be mediated by the sequential action of human DNA polymerases (Pols) iota and kappa, in which Poliota incorporates either pyrimidine opposite gamma-HOPdG, but Polkappa extends only from the cytosine. Since gamma-HOPdG can adopt either a ring-closed cyclic form or a ring-opened form in DNA, to better understand the mechanisms that Pols iota and kappa employ to promote replication through this lesion, we have examined the ability of these polymerases to replicate through the structural analogs of gamma-HOPdG that are permanently either ring closed or ring opened. Our studies with these model adducts show that whereas the ring-opened form of gamma-HOPdG is not inhibitory to synthesis by human Pols eta, iota, or kappa, only Poliota is able to incorporate nucleotides opposite the ring-closed form, which is known to adopt a syn conformation in DNA. From these studies, we infer that (i) Pols eta, iota, and kappa have the ability to proficiently replicate through minor-groove DNA lesions that do not perturb the Watson-Crick hydrogen bonding of the template base with the incoming nucleotide, and (ii) Poliota can accommodate a minor-groove-adducted template purine which adopts a syn conformation in DNA and forms a Hoogsteen base pair with the incoming nucleotide.

Cervical specimen order and performance measures of Chlamydia trachomatis diagnostic testing

The orders of three endocervical specimens of 3,561 women for Chlamydia trachomatis testing were randomized to determine whether test performance measures of two nucleic acid amplification tests and a DNA probe were affected by swab order. Specimen collection order did not appear to affect the diagnostic accuracy of these tests.

Production of oxygen by electronically induced dissociations in ice

A solid-state chemical model is given for the production of O2 by electronic excitation of ice, a process that occurs on icy bodies in the outer solar system. Based on a review of the relevant available laboratory data, we propose that a trapped oxygen atom-water complex is the principal precursor for the formation of molecular oxygen in low-temperature ice at low fluences. Oxygen formation then occurs through direct excitation of this complex or by its reaction with a freshly produced, nonthermal O from an another excitation event. We describe a model for the latter process that includes competition with precursor destruction and the effect of sample structure. This allows us to put the ultraviolet photon, low-energy electron, and fast-ion experiments on a common footing for the first time. The formation of the trapped oxygen atom precursor is favored by the preferential loss of molecular hydrogen and is quenched by reactions with mobile H. The presence of impurity scavengers can limit the trapping of O, leading to the formation of oxygen-rich molecules in ice. Rate equations that include these reactions are given and integrated to obtain an analytic approximation for describing the experimental results on the production and loss of molecular oxygen from ice samples. In the proposed model, the loss rate varies, roughly, inversely with solid-state defect density at low temperatures, leading to a yield that increases with increasing temperature as observed. Cross sections obtained from fits of the model to laboratory data are evaluated in light of the proposed solid-state chemistry.

The break-even point: when medical advances are less important than improving the fidelity with which they are delivered

Society invests billions of dollars in the development of new drugs and technologies but comparatively little in the fidelity of health care, that is, improving systems to ensure the delivery of care to all patients in need. Using mathematical arguments and a nomogram, we demonstrate that technological advances must yield dramatic, often unrealistic increases in efficacy to do more good than could be accomplished by improving fidelity. In 2 examples (the development of anti-platelet agents and statins), we show that enhanced efficacy failed to achieve the health gains that would have occurred by delivering older agents to all eligible patients. Society's huge investment in technological innovations that only modestly improve efficacy, by consuming resources needed for improved delivery of care, may cost more lives than it saves. The misalignment of priorities is driven partly by the commercial interests of industry and by the public's appetite for technological breakthroughs, but health outcomes ultimately suffer. Health, economic, and moral arguments make the case for spending less on technological advances and more on improving systems for delivering care.

Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA polymerase activity but no DNA polymerase activity

The Saccharomyces cerevisiae Trf4 and Trf5 proteins are members of a distinct family of eukaryotic DNA polymerase beta-like nucleotidyltransferases, and a template-dependent DNA polymerase activity has been reported for Trf4. To define the nucleotidyltransferase activities associated with Trf4 and Tr5, we purified these proteins from yeast cells and show that whereas both proteins exhibit a robust poly(A) polymerase activity, neither of them shows any evidence of a DNA polymerase activity. The poly(A) polymerase activity, as determined for Trf4, is strictly Mn2+ dependent and highly ATP specific, incorporating AMP onto the free 3'-hydroxyl end of an RNA primer. Unlike the related poly(A) polymerases from other eukaryotes, which are located in the cytoplasm and regulate the stability and translation efficiency of specific mRNAs, the Trf4 and Trf5 proteins are nuclear, and a multiprotein complex associated with Trf4 has been recently shown to polyadenylate a variety of misfolded or inappropriately expressed RNAs which activate their degradation by the exosome. To account for the effects of Trf4/Trf5 proteins on the various aspects of DNA metabolism, including chromosome condensation, DNA replication, and sister chromatid cohesion, we suggest an additional and essential role for the Trf4 and Trf5 protein complexes in generating functional mRNA poly(A) tails in the nucleus.

Rev1 employs a novel mechanism of DNA synthesis using a protein template

The Rev1 DNA polymerase is highly specialized for the incorporation of C opposite template G. We present here the crystal structure of yeast Rev1 bound to template G and incoming 2'-deoxycytidine 5'-triphosphate (dCTP), which reveals that the polymerase itself dictates the identity of the incoming nucleotide, as well as the identity of the templating base. Template G and incoming dCTP do not pair with each other. Instead, the template G is evicted from the DNA helix, and it makes optimal hydrogen bonds with a segment of Rev1. Also, unlike other DNA polymerases, incoming dCTP pairs with an arginine rather than the templating base, which ensures the incorporation of dCTP over other incoming nucleotides. This mechanism provides an elegant means for promoting proficient and error-free synthesis through N2-adducted guanines that obstruct replication.

Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function

This review focuses on eukaryotic translesion synthesis (TLS) DNA polymerases, and the emphasis is on Saccharomyces cerevisiae and human Y-family polymerases (Pols) eta, iota, kappa, and Rev1, as well as on Polzeta, which is a member of the B-family polymerases. The fidelity, mismatch extension ability, and lesion bypass efficiencies of these different polymerases are examined and evaluated in the context of their structures. One major conclusion is that, despite the overall similarity of basic structural features among the Y-family polymerases, there is a high degree of specificity in their lesion bypass properties. Some are able to bypass a particular DNA lesion, whereas others are efficient at only the insertion step or the extension step of lesion bypass. This functional divergence is related to the differences in their structures. Polzeta is a highly specialized polymerase specifically adapted for extending primer termini opposite from a diverse array of DNA lesions, and depending upon the DNA lesion, it contributes to lesion bypass in a mutagenic or in an error-free manner. Proliferating cell nuclear antigen (PCNA) provides the central scaffold to which TLS polymerases bind for access to the replication ensemble stalled at a lesion site, and Rad6-Rad18-dependent protein ubiquitination is important for polymerase exchange.

Distinct mechanisms of cis-syn thymine dimer bypass by Dpo4 and DNA polymerase eta

UV-light-induced cyclobutane pyrimidine dimers (CPDs) present a severe block to synthesis by replicative DNA polymerases (Pols), whereas Poleta promotes proficient and error-free replication through CPDs. Although the archael Dpo4, which, like Poleta, belongs to the Y family of DNA Pols, can also replicate through a CPD, it is much less efficient than Poleta. The x-ray crystal structure of Dpo4 complexed with either the 3'-thymine (T) or the 5' T of a cis-syn TT dimer has indicated that, whereas the 3' T of the dimer forms a Watson-Crick base pair with the incoming dideoxy ATP, the 5' T forms a Hoogsteen base pair with the dideoxy ATP in syn conformation. Based upon these observations, a similar mechanism involving Hoogsteen base pairing of the 5' T of the dimer with the incoming A has been proposed for Poleta. Here we examine the mechanisms of CPD bypass by Dpo4 and Poleta using nucleotide analogs that specifically disrupt the Hoogsteen or Watson-Crick base pairing. Our results show that both Dpo4 and Poleta incorporate dATP opposite the 5' T of the CPD via Watson-Crick base pairing and not by Hoogsteen base pairing. Furthermore, opposite the 3' T of the dimer, the two Pols differ strikingly in the mechanisms of dATP incorporation, with Dpo4 incorporating opposite an abasic-like intermediate and Poleta using the normal Watson-Crick base pairing. These observations have important implications for the mechanisms used for the inefficient vs. efficient bypass of CPDs by DNA Pols.

Osteoradionecrosis of the cervical spine resulting from radiotherapy for primary head and neck malignancies: operative and nonoperative management

✓ Osteoradionecrosis is a process of dysvascular bone necrosis and fibrous replacement following exposure to high doses of radiation. The poorly vascularized necrotic tissue may cause pain and/or instability, and it cannot resist infection well, which may result in secondary osteomyelitis. When these processes affect the cervical spine, the resulting instability and neurological deficits can be devastating, and immediate reestablishment of spinal stability is paramount. Reconstruction of the cervical spine can be particularly challenging in this subgroup of patients in whom the spine is poorly vascularized after radical surgery, high-dose irradiation, and infection. The authors report three cases of cervical spine osteoradionecrosis following radiotherapy for primary head and neck malignancies. Two patients suffered secondary osteomyelitis, severe spinal deformity, and spinal cord compression. These patients underwent surgery in which a vascularized fibular graft and instrumentation were used to reconstruct the cervical spine; subsequently hyperbaric oxygen (HBO) therapy was instituted. Fusion occurred, spinal stability was restored, and neurological dysfunction resolved at the 2- and 4-year follow-up examinations, respectively. The third patient experienced pain and dysphagia but did not have osteomyelitis, spinal instability, or neurological deficits. He underwent HBO therapy alone, with improved symptoms and imaging findings. Hyperbaric oxygen is an essential part of treatment for osteoradionecrosis and may be sufficient by itself for uncomplicated cases, but surgery is required for patients with spinal instability, spinal cord compression, and/or infection. A vascularized fibular bone graft is a very helpful adjunct in these patients because it adds little morbidity and may increase the rate of spinal fusion.

Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota

Because of the near geometric identity of Watson-Crick (W-C) GxC and AxT base pairs, a given DNA polymerase forms the four possible correct base pairs with nearly identical catalytic efficiencies. However, human DNA polymerase iota (Pol iota), a member of the Y family of DNA polymerases, exhibits a marked template specificity, being more efficient at incorporating the correct nucleotide opposite template purines than opposite pyrimidines. By using 7-deazaadenine and 7-deazaguanine as the templating residues, which disrupt Hoogsteen base pair formation, we show that, unlike the other DNA polymerases belonging to the A, B, or Y family, DNA synthesis by Pol iota is severely inhibited by these N7-modified bases. These observations provide biochemical evidence that, during normal DNA synthesis, template purines adopt a syn conformation in the Pol iota active site, enabling the formation of a Hoogsteen base pair with the incoming pyrimidine nucleotide. Additionally, mutational studies with Leu-62, which lies in close proximity to the templating residue in the Pol iota ternary complex, have indicated that both factors, steric constraints within the active site and the stability provided by the hydrogen bonds in the Hoogsteen base pair, contribute to the efficiency of correct nucleotide incorporation opposite template purines by Pol iota.

A single domain in human DNA polymerase iota mediates interaction with PCNA: implications for translesion DNA synthesis

DNA polymerases (Pols) of the Y family rescue stalled replication forks by promoting replication through DNA lesions. Humans have four Y family Pols, eta, iota, kappa, and Rev1, of which Pols eta, iota, and kappa have been shown to physically interact with proliferating cell nuclear antigen (PCNA) and be functionally stimulated by it. However, in sharp contrast to the large increase in processivity that PCNA binding imparts to the replicative Pol, Poldelta, the processivity of Y family Pols is not enhanced upon PCNA binding. Instead, PCNA binding improves the efficiency of nucleotide incorporation via a reduction in the apparent K(m) for the nucleotide. Here we show that Poliota interacts with PCNA via only one of its conserved PCNA binding motifs, regardless of whether PCNA is bound to DNA or not. The mode of PCNA binding by Poliota is quite unlike that in Poldelta, where multisite interactions with PCNA provide for a very tight binding of the replicating Pol with PCNA. We discuss the implications of these observations for the accuracy of DNA synthesis during translesion synthesis and for the process of Pol exchange at the lesion site.

Title VII funding and physician practice in rural or low-income areas

CONTEXT

Whether Title VII funding enhances physician supply in underserved areas has not clearly been established.

PURPOSE

To determine the relation between Title VII funding in medical school, residency, or both, and the number of family physicians practicing in rural or low-income communities.

METHODS

A retrospective cross sectional analysis was carried out using the 2000 American Academy of Family Physicians physician database, Title VII funding records, and 1990 U.S. Census data. Included were 9,107 family physicians practicing in 9 nationally representative states in the year 2000.

FINDINGS

Physicians exposed to Title VII funding through medical school and residency were more likely to have their current practice in low-income communities (11.9% vs 9.9%, P< or =.02) and rural areas (24.5% vs 21.8%, P< or =.02). Physicians were more likely to practice in rural communities if they attended medical schools (24.2% vs 21.4%; P =.009) and residencies (24.0% vs 20.3%; P =.011) after the school or program had at least 5 years of Title VII funding vs before. Similar increases were not observed for practice in low-income communities. In a multivariate analysis, exposure to funding and attending an institution with more years of funding independently increased the odds of practicing in rural or low-income communities.

CONCLUSIONS

Title VII funding is associated with an increase in the family physician workforce in rural and low-income communities. This effect is temporally related to initiation of funding and independently associated with effect in a multivariate analysis, suggesting a potential causal relationship. Whereas the absolute 2% increase in family physicians in these underserved communities may seem modest, it can represent a substantial increase in access to health care for community members.

Improving the diagnostic process for deep vein thrombosis in orthopaedic outpatients

Prompt diagnosis of proximal lower extremity deep vein thrombosis in outpatients is critical because of the risk of pulmonary embolism. Our purpose was to determine the accuracy of orthopaedists' clinical decisions regarding the diagnosis of proximal deep vein thrombosis in outpatients. A nationally representative random sample of 2300 orthopaedists received a survey of six clinical vignettes. They were asked to estimate the probability of proximal lower extremity deep vein thrombosis using defined criteria and to specify their planned diagnostic tests. A clinical decision rule and evidence-based diagnostic test recommendations from the general literature served as the gold standard for comparison. Six-hundred seventy-six (29%) surgeons completed the survey. The orthopaedists' planned diagnostic tests differed from the gold standard, but these differences varied depending on the probability of deep vein thrombosis. For the moderate and high risk vignettes, the diagnostic test recommendations agreed with the gold standard approximately 70% of the time. With the exception of gender, no differences were found between respondents and nonrespondents. Orthopaedists' approach to the diagnosis of deep vein thrombosis in outpatients potentially could be improved by applying a clinical decision rule and current evidence on diagnostic test usage.

Composition and Dynamics of Plasma in Saturn's Magnetosphere

During Cassini's initial orbit, we observed a dynamic magnetosphere composed primarily of a complex mixture of water-derived atomic and molecular ions. We have identified four distinct regions characterized by differences in both bulk plasma properties and ion composition. Protons are the dominant species outside about 9 RS (where RS is the radial distance from the center of Saturn), whereas inside, the plasma consists primarily of a corotating comet-like mix of water-derived ions with approximately 3% N+. Over the A and B rings, we found an ionosphere in which O2+ and O+ are dominant, which suggests the possible existence of a layer of O2 gas similar to the atmospheres of Europa and Ganymede.

Impact of patient characteristics on performance of nucleic acid amplification tests and DNA probe for detection of Chlamydia trachomatis in women with genital infections

The performance of nucleic acid amplified tests (NAAT) for Chlamydia trachomatis at the cervix and in urine was examined in 3,551 women, and the impacts of clinical findings (age, endocervical and urethral inflammation, menses, and gonococcal coinfection) were assessed. Ligase chain reaction (LCR) and first-generation uniplex PCR were studied relative to an unamplified DNA probe (PACE2) and to an expanded, independent diagnostic reference standard. Relative to the expanded standard, cervical or urine LCR was generally the most sensitive test in most subgroups. Increased detection by NAAT of cervical C. trachomatis over PACE2 was highest among women without mucopurulent endocervical discharge versus those with (relative increase in positivity with cervical LCR, 46%) and among women > or =20 years old versus younger women (relative increase in positivity with cervical LCR, 45%). The sensitivity of cervical PCR was highest when mucopurulent endocervical discharge was present (84%) and highest for cervical LCR when cervical gonococcal coinfection was detected (91%). Urethral inflammation was associated with higher sensitivities of urine LCR (86 compared to 70% when inflammation was absent) and PCR (82 compared to 62% when inflammation was absent). Menses had no effect on test performance. The effects of patient characteristics on test specificities were less pronounced and were closely related to observed sensitivities. These findings support expanded use of NAAT for screening and diagnosis of C. trachomatis in diverse clinical populations of women.

Crystal structure of the catalytic core of human DNA polymerase kappa

We present the crystal structure of the catalytic core of human DNA polymerase kappa (hPolkappa), the first structure of a human Y-family polymerase. hPolkappa is implicated in the proficient extension of mispaired primer termini on undamaged DNAs, and in the extension step of lesion bypass. The structure reveals a stubby "fingers" subdomain, which despite its small size appears to be tightly restrained with respect to a putative templating base. The structure also reveals a novel "thumb" subdomain that provides a basis for the importance of the N-terminal extension unique to hPolkappa. And, most surprisingly, the structure reveals the polymerase-associated domain (PAD) juxtaposed on the dorsal side of the "palm" subdomain, as opposed to the fingers subdomain. Together, these properties suggest that the hPolkappa active site is constrained at the site of the templating base and incoming nucleotide, but the polymerase is less constrained following translocation of the lesion.

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 886,202 deaths. Achieving equity may do more for health than perfecting the technology of care.

Unwanted control: how patients in the primary care setting decide about screening for prostate cancer

Current guidelines recommend shared decision-making to determine whether the prostate-specific antigen (PSA) test should be performed. At a large family medicine practice in suburban Washington, DC, we administered a sequence of patient and physician surveys to examine the desired and actual level of patient control over PSA screening decisions and the circumstances in which they occur. Both before and after visits, patients expressed a preference for a shared approach to the PSA decision, but the actual decision involved a significant shift toward greater patient control. Almost 25% of patients reported greater decisional control than they desired. Fully 30% of the men who wanted a shared approach made the actual decision themselves. Patients prefer a shared approach to the PSA decision but report greater personal control when the decision is actually made. Further research is needed to understand this phenomenon and to better accommodate patients' desire for shared decision-making.

Retrospective statistical analysis of lyophilized protein formulations of progenipoietin using PLS: Determination of the critical parameters for long-term storage stability

Although certain criteria have become recognized as being essential for a stable lyophilized formulation, the relative importance of different stability criteria has not been demonstrated quantitatively. This study uses multivariate statistical methods to determine the relative importance of certain formulation variables that affect long-term storage stability of a therapeutic protein. Using the projection to latent structures (PLS) method, a retrospective analysis was conducted of 18 formulations of progenipoietin (ProGP), a potential protein therapeutic agent. The relative importance of composition, pH, maintenance of protein structure (as determined by infrared (IR) spectroscopy), and thermochemical properties of the glassy state (as measured by differential scanning calorimetry (DSC)) were evaluated. Various stability endpoints were assessed and validated models constructed for each using the PLS method. Retention of parent protein and the appearance of degradation products could be adequately modeled using PLS. The models demonstrate the importance of retention of native structure in the solid state and controlling the pH. The relative importance of T(g) in affecting storage stability was low, as all of the samples had T(g) values above the highest storage temperature (40 degrees C). However, other indicators of molecular mobility in the solid state, such as change in DeltaC(p) upon annealing, appear to be important, even for storage below T(g). For the first time, the relative importance of certain properties in controlling long-term storage stability could be assessed quantitatively. In general, the most important parameters appear to be pH and retention of native structure in the solid state. However, for some stability endpoints, the composition (concentration of protein or various excipients), as well as some DSC parameters, were found to be significant in predicting long-term stability.

Efficient and error-free replication past a minor-groove N2-guanine adduct by the sequential action of yeast Rev1 and DNA polymerase zeta

Rev1, a member of the Y family of DNA polymerases, functions in lesion bypass together with DNA polymerase zeta (Pol zeta). Rev1 is a highly specialized enzyme in that it incorporates only a C opposite template G. While Rev1 plays an indispensable structural role in Pol zeta-dependent lesion bypass, the role of its DNA synthetic activity in lesion bypass has remained unclear. Since interactions of DNA polymerases with the DNA minor groove contribute to the nearly equivalent efficiencies and fidelities of nucleotide incorporation opposite each of the four template bases, here we examine the possibility that unlike other DNA polymerases, Rev1 does not come into close contact with the minor groove of the incipient base pair, and that enables it to incorporate a C opposite the N(2)-adducted guanines in DNA. To test this idea, we examined whether Rev1 could incorporate a C opposite the gamma-hydroxy-1,N(2)-propano-2'deoxyguanosine DNA minor-groove adduct, which is formed from the reaction of acrolein with the N(2) of guanine. Acrolein, an alpha,beta-unsaturated aldehyde, is generated in vivo as the end product of lipid peroxidation and from other oxidation reactions. We show here that Rev1 efficiently incorporates a C opposite this adduct from which Pol zeta subsequently extends, thereby completing the lesion bypass reaction. Based upon these observations, we suggest that an important role of the Rev1 DNA synthetic activity in lesion bypass is to incorporate a C opposite the various N(2)-guanine DNA minor-groove adducts that form in DNA.

Requirement of yeast Rad1-Rad10 nuclease for the removal of 3'-blocked termini from DNA strand breaks induced by reactive oxygen species

The Rad1-Rad10 nuclease of yeast and its human counterpart ERCC1-XPF are indispensable for nucleotide excision repair, where they act by cleaving the damaged DNA strand on the 5'-side of the lesion. Intriguingly, the ERCC1- and XPF-deficient mice show a severe postnatal growth defect and they die at approximately 3 wk after birth. Here we present genetic and biochemical evidence for the requirement of Rad1-Rad10 nuclease in the removal of 3'-blocked termini from DNA strand breaks induced on treatment of yeast cells with the oxidative DNA damaging agent H(2)O(2). Our genetic studies indicate that 3'-blocked termini are removed in yeast by the three competing pathways that involve the Apn1, Apn2, and Rad1-Rad10 nucleases, and we show that the Rad1-Rad10 nuclease proficiently cleaves DNA modified with a 3'-phosphoglycolate terminus. From these observations, we infer that deficient removal of 3'-blocking groups formed from the action of oxygen free radicals generated during normal cellular metabolism is the primary underlying cause of the inviability of apn1Delta apn2Delta rad1Delta and apn1Deltaapn2Delta rad10Delta mutants and that such a deficiency accounts also for the severe growth defects of ERCC1- and XPF-deficient mice.

Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing

Almost all DNA polymerases show a strong preference for incorporating the nucleotide that forms the correct Watson-Crick base pair with the template base. In addition, the catalytic efficiencies with which any given polymerase forms the four possible correct base pairs are roughly the same. Human DNA polymerase-iota (hPoliota), a member of the Y family of DNA polymerases, is an exception to these rules. hPoliota incorporates the correct nucleotide opposite a template adenine with a several hundred to several thousand fold greater efficiency than it incorporates the correct nucleotide opposite a template thymine, whereas its efficiency for correct nucleotide incorporation opposite a template guanine or cytosine is intermediate between these two extremes. Here we present the crystal structure of hPoliota bound to a template primer and an incoming nucleotide. The structure reveals a polymerase that is 'specialized' for Hoogsteen base-pairing, whereby the templating base is driven to the syn conformation. Hoogsteen base-pairing offers a basis for the varied efficiencies and fidelities of hPoliota opposite different template bases, and it provides an elegant mechanism for promoting replication through minor-groove purine adducts that interfere with replication.

Diagnosis of lower-extremity deep vein thrombosis in outpatients with musculoskeletal disorders: a national survey study of physical therapists

BACKGROUND AND PURPOSE

Prompt identification of outpatients who may have proximal lower-extremity deep vein thrombosis (PDVT) is important, in part, because of the risk of pulmonary embolism. The purposes of our study were to determine the degree of accuracy of physical therapists' estimates of the probability of PDVT in hypothetical patient vignettes and to determine whether physical therapists would contact the referring physician about the hypothetical patients' condition as recommended in published evidence.

SUBJECTS AND METHODS

A survey instrument consisting of 6 vignettes was sent to a nationally representative random sample of 1,500 physical therapists. The clinical decision rule developed by Wells and colleagues served as the gold standard for PDVT probability.

RESULTS

A total of 969 (65% response rate) physical therapists completed the survey. We found no evidence of nonresponse bias. For the 2 high-probability vignettes, 87% and 64% of the physical therapists underestimated the probability of PDVT. For the 2 high-probability cases, 32% and 27% of the physical therapists reported that they would not have contacted the referring physician. For the 2 moderate-probability cases, 15% and 30% of the physical therapists would not have contacted the referring physician. Therapist experience, certification status, place of practice, and region of the country did not explain the findings.

DISCUSSION AND CONCLUSION

The care of outpatients who are at risk for PDVT could potentially be improved by use of the clinical decision rule developed by Wells and colleagues, although more study is warranted.

Efficient and error-free replication past a minor-groove DNA adduct by the sequential action of human DNA polymerases iota and kappa

DNA polymerase iota (Poliota) is a member of the Y family of DNA polymerases, which promote replication through DNA lesions. The role of Poliota in lesion bypass, however, has remained unclear. Poliota is highly unusual in that it incorporates nucleotides opposite different template bases with very different efficiencies and fidelities. Since interactions of DNA polymerases with the DNA minor groove provide for the nearly equivalent efficiencies and fidelities of nucleotide incorporation opposite each of the four template bases, we considered the possibility that Poliota differs from other DNA polymerases in not being as sensitive to distortions of the minor groove at the site of the incipient base pair and that this enables it to incorporate nucleotides opposite highly distorting minor-groove DNA adducts. To check the validity of this idea, we examined whether Poliota could incorporate nucleotides opposite the gamma-HOPdG adduct, which is formed from an initial reaction of acrolein with the N(2) of guanine. We show here that Poliota incorporates a C opposite this adduct with nearly the same efficiency as it does opposite a nonadducted template G residue. The subsequent extension step, however, is performed by Polkappa, which efficiently extends from the C incorporated opposite the adduct. Based upon these observations, we suggest that an important biological role of Poliota and Polkappa is to act sequentially to carry out the efficient and accurate bypass of highly distorting minor-groove DNA adducts of the purine bases.

Opposing effects of ubiquitin conjugation and SUMO modification of PCNA on replicational bypass of DNA lesions 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 zeta (Polzeta) and Poleta and postreplicational repair mediated by the Mms2-Ubc13 ubiquitin-conjugating enzyme and Rad5. Here we report our studies with a proliferating cell nuclear antigen (PCNA) mutation, pol30-119, which results from a change of the lysine 164 residue to arginine. It has been shown recently that following treatment of yeast cells with DNA-damaging agents, the lysine 164 residue of PCNA becomes monoubiquitinated in a Rad6-Rad18-dependent manner and that subsequently this PCNA residue is polyubiquitinated via a lysine 63-linked ubiquitin chain in an Mms2-Ubc13-, Rad5-dependent manner. PCNA is also modified by SUMO conjugation at the lysine 164 residue. Our genetic studies with the pol30-119 mutation show that in addition to conferring a defect in Polzeta-dependent UV mutagenesis and in Poleta-dependent TLS, this PCNA mutation inhibits postreplicational repair of discontinuities that form in the newly synthesized strand across from UV lesions. In addition, we provide evidence for the activation of the RAD52 recombinational pathway in the pol30-119 mutant and we infer that SUMO conjugation at the lysine 164 residue of PCNA has a role in suppressing the Rad52-dependent postreplicational repair pathway.

Energy loss by keV ions in silicon

Using silicon photodiodes with an ultrathin passivation layer, the average total energy lost to silicon target electrons (electronic stopping) by incident low energy ions and the recoil target atoms they generate is directly measured. We find that the total electronic energy deposition and the ratio of the total nuclear to electronic stopping powers for the incident ions and their recoils each follow a simple, universal representation, thus enabling systematic prediction of ion-induced effects in silicon. We also observe a velocity threshold at 0.05 a.u. for the onset of electronic stopping.

Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States

Chlamydia trachomatis is a major cause of ocular and sexually transmitted diseases worldwide. While much of our knowledge about its genetic diversity comes from serotyping or ompA genotyping, no quantitative assessment of genetic diversity within serotypes has been performed. To accomplish this, 507 urogenital samples from a multicenter U.S. study were analyzed by phylogenetic and statistical modeling. No B, Da, or I serotypes were represented. Based on our analyses, all but one previous urogenital B serotype was identified as Ba. This, coupled with the lack of B serotypes in our population, suggests that B has specific tropism for ocular mucosa. We identified a Ba/D recombinant (putative crossover nucleotide 477; P < 0.0001) similar to a B/D mosaic we described previously from an African trachoma patient. Computational analyses of the Ba/D recombinant indicated that upstream changes were less important for tissue tropism than downstream incorporation of the D sequence. Since most serotypes had nonsynonymous/synonymous ratios of <1.0, the major outer membrane protein, encoded by ompA, has many functional constraints and is under purifying selection. Surprisingly, all serotype groups except for J had a unimodal population structure indicating rapid clonal expansion. Of the groups with a unimodal structure, E and Ia and, to a lesser extent, G and K were prevalent, had infrequent incorporation of mutations, and, compared to other groups, had a relatively greater degree of diversifying selection, consistent with a selective sweep of mutations within these groups. Collectively, these data suggest a diverse evolutionary strategy for different serogroups of the organism.

Dpo4 is hindered in extending a G.T mismatch by a reverse wobble

The ability or inability of a DNA polymerase to extend a mispair directly affects the establishment of genomic mutations. We report here kinetic analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus solfataricus, to extend from all mispairs opposite a template G or T. Dpo4 is equally inefficient at extending these mispairs, which include, surprisingly, a G.T mispair expected to conform closely to Watson-Crick geometry. To elucidate the basis of this, we solved the structure of Dpo4 bound to G.T-mispaired primer template in the presence of an incoming nucleotide. As a control, we also determined the structure of Dpo4 bound to a matched A-T base pair at the primer terminus. The structures offer a basis for the low efficiency of Dpo4 in extending a G.T mispair: a reverse wobble that deflects the primer 3'-OH away from the incoming nucleotide.

Comparing the use of short-acting and long-acting calcium channel blockers in an HMO

One of the questions surrounding the controversy over the risks of MI among hypertensives taking calcium channel blockers (CCBs) is the dosage form, and whether the short-acting form may be more likely than the long-acting to increase the risk of MI. This preliminary study compared HMO members receiving the two dosage forms by sociodemographic and clinical characteristics, and by utilization (hospital, office visits, emergency room, outside of HMO services) prior to and during CCB use. The sampling frame was members with one or more dispensings for a CCB 1990 through 1994. Incident users were those who received one or more CCB dispensings and no cardiovascular disease-related drugs the year prior to their first dispensing of a CCB. CCB users were those who had at least 90 days of continuous CCB use. Short-acting outnumbered long-acting users by eight to one. Few incident users of long-acting CCBs were found. Among incident users, diagnoses and comorbidities were similar. In general, short-acting users appeared to have less risk of exposure to heart-related medications, but similar risks of exposure to non-heart-related drugs and to utilization of the various services during the year prior to first use. The odds of being exposed to heart-related medications and non-heart related medications and use of services during periods of use of CCBs were similar in general, but where differences were observed, the odds of being exposed were less among short-acting users. Users of the two dosage forms in this setting prior to reports questioning the safety of short-acting CCBs were different quantitatively and qualitatively making a retrospective comparative study difficult, perhaps not possible, due to substantial selection bias among users. Further patient selection bias has also undoubtedly occurred subsequent to the reports. The final answer to the relative safety and effectiveness of the different dosage forms of calcium channel blockers is likely to have come from randomized clinical trials.

Human DNA polymerase iota utilizes different nucleotide incorporation mechanisms dependent upon the template base

Human DNA polymerase iota (Poliota) is a member of the Y family of DNA polymerases involved in translesion DNA synthesis. Poliota is highly unusual in that it possesses a high fidelity on template A, but has an unprecedented low fidelity on template T, preferring to misincorporate a G instead of an A. To understand the mechanisms of nucleotide incorporation opposite different template bases by Poliota, we have carried out pre-steady-state kinetic analyses of nucleotide incorporation opposite templates A and T. These analyses have revealed that opposite template A, the correct nucleotide is preferred because it is bound tighter and is incorporated faster than the incorrect nucleotides. Opposite template T, however, the correct and incorrect nucleotides are incorporated at very similar rates, and interestingly, the greater efficiency of G misincorporation relative to A incorporation opposite T arises predominantly from the tighter binding of G. Based on these results, we propose that the incipient base pair is accommodated differently in the active site of Poliota dependent upon the template base and that when T is the templating base, Poliota accommodates the wobble base pair better than the Watson-Crick base pair.

The mechanism of nucleotide incorporation by human DNA polymerase eta differs from that of the yeast enzyme

DNA polymerase eta (Poleta) catalyzes the efficient and accurate synthesis of DNA opposite cyclobutane pyrimidine dimers, and inactivation of Poleta in humans causes the cancer-prone syndrome, the variant form of xeroderma pigmentosum. Pre-steady-state kinetic studies of yeast Poleta have indicated that the low level of fidelity of this enzyme results from a poorly discriminating induced-fit mechanism. Here we examine the mechanistic basis of the low level of fidelity of human Poleta. Because the human and yeast enzymes behave similarly under steady-state conditions, we expected these enzymes to utilize similar mechanisms of nucleotide incorporation. Surprisingly, however, we find that human Poleta differs from the yeast enzyme in several important respects. The human enzyme has a 50-fold-faster rate of nucleotide incorporation than the yeast enzyme but binds the nucleotide with an approximately 50-fold-lower level of affinity. This lower level of binding affinity might provide a means of regulation whereby the human enzyme remains relatively inactive except when the cellular deoxynucleoside triphosphate concentrations are high, as may occur during DNA damage, thereby avoiding the mutagenic consequences arising from the inadvertent action of this enzyme during normal DNA replication.

Risk factors for Plantar fasciitis: a matched case-control study

BACKGROUND

Plantar fasciitis is one of the more common soft-tissue disorders of the foot, yet little is known about its etiology. The purpose of the present study was to use an epidemiological design to determine whether risk factors for plantar fasciitis could be identified. Specifically, we examined the risk factors of limited ankle dorsiflexion with the knee extended, obesity, and time spent weight-bearing.

METHODS

We used a matched case-control design, with two controls for each patient. The matching criteria were age and gender. We identified fifty consecutive patients with unilateral plantar fasciitis who met the inclusion criteria. The data that were collected included height, weight, whether the subject spent the majority of the workday weight-bearing, and whether the subject was a jogger or runner. We used a reliable goniometric method to measure passive ankle dorsiflexion bilaterally. The main outcome measure was the adjusted odds ratio of plantar fasciitis associated with varying degrees of limitation of ankle dorsiflexion, different levels of body mass, and the subjects' reports on weight-bearing.

RESULTS

Individuals with </=0 degrees of dorsiflexion had an odds ratio of 23.3 (95% confidence interval, 4.3 to 124.4) when compared with the referent group of individuals who had >10 degrees of ankle dorsiflexion. Individuals who had a body-mass index of >30 kg/m (2) had an odds ratio of 5.6 (95% confidence interval, 1.9 to 16.6) when compared with the referent group of individuals who had a body-mass index of </=25 kg/m (2). Individuals who reported that they spent the majority of their workday on their feet had an odds ratio of 3.6 (95% confidence interval, 1.3 to 10.1) when compared with the referent group of those who did not.

CONCLUSIONS

The risk of plantar fasciitis increases as the range of ankle dorsiflexion decreases. Individuals who spend the majority of their workday on their feet and those whose body-mass index is >30 kg/m (2) are also at increased risk for the development of plantar fasciitis. Reduced ankle dorsiflexion, obesity, and work-related weight-bearing appear to be independent risk factors for plantar fasciitis. Reduced ankle dorsiflexion appears to be the most important risk factor.

Molecular dynamics study of a bilayer electron gas: single particle properties

The single-particle dynamical properties of a strongly coupled, classical, symmetric electronic bilayer system have been investigated by molecular dynamics simulation. Results for the velocity correlation function, the single-particle scattering function, and their respective Fourier transforms have been calculated, and their behavior, as a function of the interlayer separation d, has been analyzed. The single-particle scattering function in particular, shows dramatic effects when the bilayer attains a staggered square lattice structure. This occurs when the interlayer separation is around 0.8a (a is the Wigner-Seitz radius), where our previous study showed a marked decrease in the diffusion coefficient.

Deoxynucleotide triphosphate binding mode conserved in Y family DNA polymerases

Although DNA polymerase eta (Pol eta) and other Y family polymerases differ in sequence and function from classical DNA polymerases, they all share a similar right-handed architecture with the palm, fingers, and thumb domains. Here, we examine the role in Saccharomyces cerevisiae Pol eta of three conserved residues, tyrosine 64, arginine 67, and lysine 279, which come into close contact with the triphosphate moiety of the incoming nucleotide, in nucleotide incorporation. We find that mutational alteration of these residues reduces the efficiency of correct nucleotide incorporation very considerably. The high degree of conservation of these residues among the various Y family DNA polymerases suggests that these residues are also crucial for nucleotide incorporation in the other members of the family. Furthermore, we note that tyrosine 64 and arginine 67 are functionally equivalent to the deoxynucleotide triphosphate binding residues arginine 518 and histidine 506 in T7 DNA polymerase, respectively.

The production of oxidants in Europa's surface

The oxidants produced by radiolysis and photolysis in the icy surface of Europa may be necessary to sustain carbon-based biochemistry in Europa's putative subsurface ocean. Because the subduction of oxidants to the ocean presents considerable thermodynamic challenges, we examine the formation of oxygen and related species in Europa's surface ice with the goal of characterizing the chemical state of the irradiated material. Relevant spectral observations of Europa and the laboratory data on the production of oxygen and related species are first summarized. Since the laboratory data are incomplete, we examine the rate equations for formation of oxygen and its chemical precursors by radiolysis and photolysis. Measurements and simple rate equations are suggested that can be used to characterize the production of oxidants in Europa's surface material and the chemical environment produced by radiolysis. Possible precursor molecules and the role of radical trapping are examined. The possibility of oxygen reactions on grain surfaces in Europa's regolith is discussed, and the earlier estimates of the supply of O(2) to the atmosphere are increased.

The stalling of transcription at abasic sites is highly mutagenic

Abasic (AP) sites represent one of the most frequently formed lesions in DNA. Here, we examine the consequences of the stalling of RNA polymerase II at AP sites in DNA in Saccharomyces cerevisiae. A severe inhibition of transcription occurs in strains that are defective in the removal of AP sites and that also lack the RAD26 gene, a homolog of the human Cockayne syndrome group B (CSB) gene, and, importantly, a dramatic rise in mutagenesis is incurred in such strains. From the various observations presented here, we infer that the stalling of transcription at AP sites is highly mutagenic.

Yeast DNA polymerase zeta (zeta) is essential for error-free replication past thymine glycol

DNA polymerase zeta (Polzeta) promotes the mutagenic bypass of DNA lesions in eukaryotes. Genetic studies in Saccharomyces cerevisiae have indicated that relative to the contribution of other pathways, Polzeta makes only a modest contribution to lesion bypass. Intriguingly, however, disruption of the REV3 gene, which encodes the catalytic subunit of Polzeta, causes early embryonic lethality in mice. Here, we present genetic and biochemical evidence for the requirement of yeast Polzeta for predominantly error-free replication past thymine glycol (Tg), a DNA lesion formed frequently by free radical attack. These results raise the possibility that, as in yeast, in higher eukaryotes also, Polzeta makes a major contribution to the replicative bypass of Tgs as well as other lesions that block synthesis by replicative DNA polymerases. Such a preeminent role of Polzeta in lesion bypass would ensure that rapid cell divisions continue unabated during early embryonic development, thereby minimizing the generation of DNA strand breaks, chromosome aberrations, and the ensuing apoptotic response.

Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections--2002

Since publication of CDC's 1993 guidelines (CDC, Recommendations for the prevention and management of Chlamydia trachomatis infections, 1993. MMWR 1993;42[No. RR-12]:1-39), nucleic acid amplification tests (NAATs) have been introduced as critical new tools to diagnose and treat C. trachomatis and Neisseria gonorrhoeae infections. NAATs for C. trachomatis are substantially more sensitive than previous tests. When using a NAAT, any sacrifice in performance when urine is substituted for a traditional swab specimen is limited, thus reducing dependence on invasive procedures and expanding the venues where specimens can be obtained. NAATs can also detect both C. trachomatis and N. gonorrhoeae organisms in the same specimen. However, NAATs are usually more expensive than previous tests, making test performance from an economic perspective a key consideration. This report updates the 1993 guidelines for selecting laboratory tests for C. trachomatis with an emphasis on screening men and women in the United States. (In this report, screening refers to testing persons in the absence of symptoms or signs indicating C. trachomatis or N. gonorrhoeae infection.) In addition, these guidelines consider tests from an economic perspective and expand the previous guidelines to address detection of N. gonorrhoeae as well as C. trachomatis infections. Because of the increased cost of NAATs, certain laboratories are modifying manufacturers' procedures to improve test sensitivity without incurring the full cost associated with screening with a NAAT. Such approaches addressed in these guidelines are pooling of specimens before testing with a NAAT and additional testing of specimens whose non-NAAT test result is within a gray zone. This report also addresses the need for additional testing after a positive screening test to improve the specificity of a final diagnosis. To prepare these guidelines, CDC staff identified pertinent concerns, compiled the related literature published during 1990 or later, prepared tables of evidence, and drafted recommendations. Consultants, selected for their expertise or disciplinary and organizational affiliations, reviewed the draft recommendations. These final guidelines are the recommendations of CDC staff who considered contributions from scientific consultants. These guidelines are intended for laboratorians, clinicians, and managers who must choose among the multiple available tests, establish standard operating procedures for collecting and processing specimens, interpret test results for laboratory reporting, and counsel and treat patients.

Head-to-head multicenter comparison of DNA probe and nucleic acid amplification tests for Chlamydia trachomatis infection in women performed with an improved reference standard

Few evaluations of tests for Chlamydia trachomatis have compared nucleic acid amplification tests (NAATs) with diagnostic tests other than those by culture. In a five-city study of 3,551 women, we compared the results of commercial ligase chain reaction (LCR) and PCR tests performed on cervical swabs and urine with the results of PACE 2 tests performed on cervical swabs, using independent reference standards that included both cervical swabs and urethral swab-urine specimens. Using cervical culture as a standard, the sensitivities of PACE 2, LCR, and PCR tests with cervical specimens were 78.1, 96.9, and 89.9%, respectively, and the specificities were 99.3, 97.5, and 98.2%, respectively. Using either cervical swab or urine LCR-positive tests as the standard decreased sensitivities to 60.8% for PACE 2 and to 75.8 and 74.9% for PCR with cervical swabs and urine, respectively. Specificities increased to 99.7% for PACE 2 and to 99.7 and 99.4% for PCR with cervical swabs and urine, respectively. Sensitivities with a cervical swab-urine PCR standard were 61.9% for PACE 2 and 85.5 and 80.8% for LCR with cervical swabs and urine, respectively. Specificities were 99.6% for PACE 2 and 99.0 and 98.9% for LCR with cervical swabs and urine, respectively. Cervical swab versus urine differences were significant only for PCR specificities (P = 0.034). Overall, LCR sensitivity exceeded that of PCR, and sensitivities obtained with cervical swabs exceeded those obtained with urine specimens by small amounts. These data have substantiated, using a large multicenter sample and a patient standard, that LCR and PCR tests performed on endocervical swabs and urine are superior to PACE 2 tests for screening C. trachomatis infections in women. In our study, NAATs improved the detection of infected women by 17 to 38% compared to PACE 2.

Molecular dynamics study of diffusion in a bilayer electron gas

Molecular dynamics simulations of strongly coupled, classical electronic bilayers, interacting through the Coulomb potential, have been produced and studied. Values of the plasma coupling parameter Gamma between 10 and 80 and interlayer separations d from 0.1 to 3.0, (in units of Wigner-Seitz radius), were considered. The simulation results were used to calculate the intralayer and interlayer pair correlation functions and self-diffusion of charged particles in this system. The variation of self-diffusion with Gamma and d has been analyzed, and it is found that for the largest value of Gamma, the diffusion coefficient does not increase monotonically with layer separation, but has a distinct minimum for values of d slightly less than 1.