Influence of Surface Oxygen Vacancies and Ruthenium Valence State on the Catalysis of Pyrochlore Oxides

Proton exchange membrane (PEM) water electrolysis is a promising energy storage solution by electrochemically splitting water into hydrogen fuel and oxygen. However, the sluggish kinetics, high operating potential, and corrosive acidic environment during the oxygen evolution reaction (OER) require the use of scarce and costly Ir-based oxides, tremendously hampering its large-scale commercialization. Hence, developing active and stable anode catalysts with reduced precious-metal usage is desperately essential. For the first time, we report a group of Y_2-xBa_xRu₂O₇ pyrochlore oxides and employ them in acid OER and PEM electrolyzers. We reveal the mechanism for the promoted OER performance of Ba-doped Y₂Ru₂O₇ in which partially replacing Y³⁺ by Ba²⁺ in Y₂Ru₂O₇ greatly facilitates the hole-doping effect, which generates massive oxygen vacancy and multivalence of Ru⁵⁺/Ru⁴⁺, thus boosting the OER performance of Y_2-xBa_xRu₂O₇. This work provides an effective method and paradigm for improving the electrocatalytic property of pyrochlore oxides.

Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding

RNA and DNA hairpin formation and disruption play key regulatory roles in a variety of cellular processes. The 59-nucleotide transactivation response (TAR) RNA hairpin facilitates the production of full-length transcripts of the HIV-1 genome. Yet the stability of this long, irregular hairpin becomes a liability during reverse transcription as 24 base pairs must be disrupted for strand transfer. Retroviral nucleocapsid (NC) proteins serve as nucleic acid chaperones that have been shown to both destabilize the TAR hairpin and facilitate strand annealing with its complementary DNA sequence. Yet it has remained difficult to elucidate the way NC targets and dramatically destabilizes this hairpin while only weakly affecting the annealed product. In this work, we used optical tweezers to measure the stability of TAR and found that adding NC destabilized the hairpin and simultaneously caused a distinct change in both the height and location of the energy barrier. This data was matched to an energy landscape predicted from a simple theory of definite base pair destabilization. Comparisons revealed the specific binding sites found by NC along the irregular TAR hairpin. Furthermore, specific binding explained both the unusual shift in the transition state and the much weaker effect on the annealed product. These experiments illustrate a general method of energy landscape transformation that exposes important physical insights.

HIV restriction factor APOBEC3G binds in multiple steps and conformations to search and deaminate single-stranded DNA

APOBEC3G (A3G), an enzyme expressed in primates with the potential to inhibit human immunodeficiency virus type 1 (HIV-1) infectivity, is a single-stranded DNA (ssDNA) deoxycytidine deaminase with two domains, a catalytically active, weakly ssDNA binding C-terminal domain (CTD) and a catalytically inactive, strongly ssDNA binding N-terminal domain (NTD). Using optical tweezers, we measure A3G binding a single, long ssDNA substrate under various applied forces to characterize the binding interaction. A3G binds ssDNA in multiple steps and in two distinct conformations, distinguished by degree of ssDNA contraction. A3G stabilizes formation of ssDNA loops, an ability inhibited by A3G oligomerization. Our data suggests A3G securely binds ssDNA through the NTD, while the CTD samples and potentially deaminates the substrate. Oligomerization of A3G stabilizes ssDNA binding but inhibits the CTD's search function. These processes explain A3G's ability to efficiently deaminate numerous sites across a 10,000 base viral genome during the reverse transcription process.

Coronary artery calcification is associated with mortality independent of pulmonary embolism severity: a retrospective cohort study

AIM

To assess coronary artery calcification (CAC) and vascular calcification in patients with pulmonary embolism (PE) and correlate this with mortality.

MATERIALS AND METHODS

PE severity was quantified using computed tomography pulmonary angiography (CTPA) in 400 consecutive cases using the modified Miller score (1-5, mild; 6-11, moderate; 12-16, severe). Right ventricle strain was assessed using the right/left ventricle diameter (RV/LV) ratio. CAC score (CACS) was assessed using a four-point scale (CACS mild 1-3, moderate 4-8, severe 9-12) for each vessel and summed to give the total CACS. Follow-up for mortality was obtained at 3 years.

RESULTS

PE severity was classified as mild in 48%, moderate in 21%, and severe in 32% of cases. The median modified Miller score was 6 (Interquartile range [IQR] 2, 14) and median total CACS was 2 (IQR 0, 7). All-cause mortality occurred in 128 (32%) patients. Patients with CAC were three times more likely to die than patients without CAC (Hazard ratio [HR] 2.96; 95% CI 1.84, 4.77; p<0.001), and patients with severe CAC were at the highest risk (HR 4.62; 95% CI 2.73, 7.83, p<0.001). Gender, modified Miller score and RV/LV ratio were not predictive of mortality. In multivariate analysis both CACS and age were independent predictors of 3-year all-cause mortality. Of the patients with CAC who died, the presence of coronary artery disease was only documented in 34 (32%).

CONCLUSION

CACS is an independent predictor of all-cause mortality in patients with PE, and has important implications for subsequent patient management.

1269Dual antiplatelet therapy to inhibit myocardial injury in patients with high-risk coronary artery plaque: a randomized controlled trial

Background

High-risk coronary atherosclerotic plaque is associated with higher plasma troponin concentrations suggesting ongoing myocardial injury that may be a target for dual antiplatelet therapy.

Purpose

To determine whether ticagrelor reduces high-sensitivity troponin I concentrations in patients with established coronary artery disease and high-risk coronary plaque with 18F-fluoride uptake.

Methods

In a randomized double-blind placebo-controlled trial, patients with multivessel coronary artery disease underwent coronary 18F-fluoride positron emission tomography-computed tomography and measurement of high-sensitivity cardiac troponin I and were randomized (1:1) to ticagrelor 90 mg twice daily or matched placebo. The primary endpoint was troponin I concentration at 30 days in patients with increased coronary 18F-fluoride uptake.

Results

In total, 202 patients were randomized and 191 met the pre-specified criteria for inclusion in the primary analysis. In patients with increased coronary 18F-fluoride uptake (n=120/191) there was no evidence that ticagrelor had an effect on plasma troponin concentrationsat 30 days (ratio of geometric means for ticagrelor versusplacebo, 1.11, [95% confidence interval 0.90 to 1.36], p=0.32) (Table 1). Over 1 year, ticagrelor had no effect on troponin concentrations in patients with increased coronary 18F-fluoride uptake (ratio of geometric means, 0.86, 95% confidence interval 0.63 to 1.17, p=0.33).

Table 1 Adjusted Geometric Mean (GSE) Ratio of Geometric Means p-value Ticagrelor Placebo (95% CI) Cardiac troponin I, ng/L (18F-fluoride activity) 3.8 (1.1) 3.4 (1.1) 1.11 (0.90 to 1.36) 0.32 Cardiac Troponin I, ng/L (No 18F-fluoride activity) 2.4 (1.1) 2.3 (1.1) 1.02 (0.80 to 1.31) 0.87 Plasma high-sensitivity cardiac troponin I concentration (ng/L) at 30 days for the per-protocol population.Estimates are back transformed estimates from analysis of log transformed values at 30 days adjusting for age, sex and log transformed baseline troponin. Ratio of geometric means is Ticagrelor divided by Placebo. GSE, geometric standard error.

Conclusions

Dual antiplatelet therapy with ticagrelor does not reduce plasma troponin concentrations in patients with coronary 18F-fluoride uptake. This suggests that subclinical plaque thrombosis does not contribute to ongoing myocardial injury in this setting.

Clinical Trials Study ID: NCT02110303Study ID: NCT02110303

Acknowledgement/Funding

Wellcome Trust Senior Investigator Award WT103782AIA

P2237National trends in coronary artery disease imaging

Background

The 2010 National Institute of Clinical Excellence (NICE) Clinical Guideline 95 (CG95) recommended coronary computed tomographic angiography (CTA) for low-intermediate risk patients with stable chest pain. The indications for CTA broadened substantially in the 2016 update, which recommended CTA for all patients with possible angina and diagnostic uncertainty.

Purpose

To examine trends in the use of imaging for the investigation of coronary artery disease (CAD) in England in the years before and after the 2016 CG95 guideline update.

Methods

Numbers of invasive coronary angiography (ICA), single positron emission tomography (SPECT), stress echocardiography (SE), CTA, and positron emission tomography (PET) scans performed from 2012–2018 were extracted from a national database of imaging procedures performed in England. Per capita average annual growth was calculated at a national and healthcare provider level, and comparisons were made before and after the 2016 CG95 update. Healthcare providers with greater than median CTA growth were compared to those with less than median growth to ascertain the impact of CTA on other forms of CAD investigation. Total healthcare provider costs for imaging were calculated using NHS tariff costs.

Results

From 2012–2018, 1,792,655 imaging examinations were performed for the investigation of CAD, with an overall annualized growth rate of 4%. Average annual growth (per 100,000 population per year) from 2012–2018 was 1±31% for ICA, 28±39% for CTA, −11±22% for SPECT, 0±1% for PET, 1±2% for SE and 5±16% for MRI. Following the 2016 CG95 update, there was an increase in the year-to-year average annual growth of CTA scans performed (53±79 versus 2±53 tests/100,000/yr, p<0.001) compared with a fall in the rate of ICA use (−13±48 versus +5±36 tests/100,000/yr, p=0.03). SPECT underwent a consistent fall in utilisation over the study period, with an average annual growth rate of −4%, with no difference before or after the 2016 CG95 update (P>0.1). Rates of change in the utilization of SE, PET, and MRI did not change following the introduction of the 2016 CG95 update. Regions with an above median average annual growth in CTA exhibited a greater decline in SPECT use (−19±28 versus −4±11 tests/100,000/yr, p=0.037) than regions with a below median growth in CTA use, with no difference in the average annual growth of ICA, SE, PET or MRI (p>0.1 for all; Figure 1). Per capita healthcare costs remained stable throughout the study period, with no significant change following CG95 (p>0.1).

Figure 1. CTA, SPECT and ICA growth rate

Conclusion

There is a clear and consistent trend towards increased imaging for the diagnosis and management of CAD. The 2016 NICE CG95 update resulted in a rise in the use of CTA, and a fall in ICA. Importantly, rates of ICA utilization fell despite a rise in CTA usage. Centres with the greatest growth in CTA had the greatest fall in SPECT utilisation and consequently, overall imaging costs were unchanged.

Single and double box HMGB proteins differentially destabilize nucleosomes

Nucleosome disruption plays a key role in many nuclear processes including transcription, DNA repair and recombination. Here we combine atomic force microscopy (AFM) and optical tweezers (OT) experiments to show that high mobility group B (HMGB) proteins strongly disrupt nucleosomes, revealing a new mechanism for regulation of chromatin accessibility. We find that both the double box yeast Hmo1 and the single box yeast Nhp6A display strong binding preferences for nucleosomes over linker DNA, and both HMGB proteins destabilize and unwind DNA from the H2A–H2B dimers. However, unlike Nhp6A, Hmo1 also releases half of the DNA held by the (H3–H4)₂ tetramer. This difference in nucleosome destabilization may explain why Nhp6A and Hmo1 function at different genomic sites. Hmo1 is enriched at highly transcribed ribosomal genes, known to be depleted of histones. In contrast, Nhp6A is found across euchromatin, pointing to a significant difference in cellular function.

Quantifying the stability of oxidatively damaged DNA by single-molecule DNA stretching

One of the most common DNA lesions is created when reactive oxygen alters guanine. 8-oxo-guanine may bind in the anti-conformation with an opposing cytosine or in the syn-conformation with an opposing adenine paired by transversion, and both conformations may alter DNA stability. Here we use optical tweezers to measure the stability of DNA hairpins containing 8-oxoguanine (8oxoG) lesions, comparing the results to predictive models of base-pair energies in the absence of the lesion. Contrasted with either a canonical guanine-cytosine or adenine-thymine pair, an 8oxoG-cytosine base pair shows significant destabilization of several k_BT. The magnitude of destabilization is comparable to guanine-thymine ‘wobble’ and cytosine-thymine mismatches. Furthermore, the measured energy of 8oxoG-adenine corresponds to theoretical predictions for guanine-adenine pairs, indicating that oxidative damage does not further destabilize this mismatch in our experiments, in contrast to some previous observations. These results support the hypothesis that oxidative damage to guanine subtly alters the direction of the guanine dipole, base stacking interactions, the local backbone conformation, and the hydration of the modified base. This localized destabilization under stress provides additional support for proposed mechanisms of enzyme repair.

Breast arterial calcification on mammography and risk of coronary artery disease: a SCOT-HEART sub-study

AIM

To assess the prevalence of breast arterial calcification (BAC) in patients who also underwent routine surveillance mammography, and to determine the association with cardiovascular risk factors, coronary artery calcification, and coronary artery disease on coronary computed tomography angiography (CCTA).

MATERIALS AND METHODS

Four hundred and five female participants were identified who had undergone CCTA and subsequent mammography in the SCOT-HEART randomised controlled trial of CCTA in patients with suspected stable angina. Mammograms were assessed visually for the presence and severity of BAC.

RESULTS

BAC was identified in 93 (23%) patients. Patients with BAC were slightly older (63±7 versus 59±8 years, p<0.001), with a higher cardiovascular risk score (19±11 versus 16±10, p=0.022) and were more likely to be non-smokers (73% versus 49%, p<0.001). In patients with BAC, coronary artery calcification was present in 58 patients (62%; relative risk [RR] 1.26, 95% confidence intervals [CI]: 1.04, 1.53; p=0.02), non-obstructive coronary artery disease in 58 (62%; RR 1.27, 95% CI: 1.04 to 1.54, p=0.02), and obstructive coronary artery disease in 19 (20%; RR 1.62, 95% CI: 0.98, 2.66; p=0.058). Patients without BAC were very unlikely to have severe coronary artery calcification (negative predictive value 95%) but the diagnostic accuracy of BAC to identify coronary artery disease was poor (AUC 0.547).

CONCLUSION

Although BAC is associated with the presence and severity of coronary artery calcification, the diagnostic accuracy to identify patients with coronary artery disease or obstructive coronary artery disease is poor.

•

Breast arterial calcification occurs in a fifth of patients referred for CCTA who tend to be older non-smokers.

•

It is associated with higher coronary artery calcium but this is predominantly dependent on age and cardiovascular risks.

•

Absence of breast arterial calcification excludes severe coronary artery calcification, negative predictive value of 95%.

DNA Intercalation Facilitates Efficient DNA-Targeted Covalent Binding of Phenanthriplatin

Phenanthriplatin, a monofunctional anticancer agent derived from cisplatin, shows significantly more rapid DNA covalent-binding activity compared to its parent complex. To understand the underlying molecular mechanism, we used single-molecule studies with optical tweezers to probe the kinetics of DNA-phenanthriplatin binding as well as DNA binding to several control complexes. The time-dependent extensions of single λ-DNA molecules were monitored at constant applied forces and compound concentrations, followed by rinsing with a compound-free solution. DNA-phenanthriplatin association consisted of fast and reversible DNA lengthening with time constant τ ≈ 10 s, followed by slow and irreversible DNA elongation that reached equilibrium in ∼30 min. In contrast, only reversible fast DNA elongation occured for its stereoisomer  trans-phenanthriplatin, suggesting that the distinct two-rate kinetics of phenanthriplatin is sensitive to the geometric conformation of the complex. Furthermore, no DNA unwinding was observed for pyriplatin, in which the phenanthridine ligand of phenanthriplatin is replaced by the smaller pyridine molecule, indicating that the size of the aromatic group is responsible for the rapid DNA elongation. These findings suggest that the mechanism of binding of phenanthriplatin to DNA involves rapid, partial intercalation of the phenanthridine ring followed by slower substitution of the adjacent chloride ligand by, most likely, the N7 atom of a purine base. The cis isomer affords the proper stereochemistry at the metal center to facilitate essentially irreversible DNA covalent binding, a geometric advantage not afforded by trans-phenanthriplatin. This study demonstrates that reversible DNA intercalation provides a robust transition state that is efficiently converted to an irreversible DNA-Pt bound state.

The role of the C-domain of bacteriophage T4 gene 32 protein in ssDNA binding and dsDNA helix-destabilization: Kinetic, single-molecule, and cross-linking studies

The model single-stranded DNA binding protein of bacteriophage T4, gene 32 protein (gp32) has well-established roles in DNA replication, recombination, and repair. gp32 is a single-chain polypeptide consisting of three domains. Based on thermodynamics and kinetics measurements, we have proposed that gp32 can undergo a conformational change where the acidic C-terminal domain binds internally to or near the single-stranded (ss) DNA binding surface in the core (central) domain, blocking ssDNA interaction. To test this model, we have employed a variety of experimental approaches and gp32 variants to characterize this conformational change. Utilizing stopped-flow methods, the association kinetics of wild type and truncated forms of gp32 with ssDNA were measured. When the C-domain is present, the log-log plot of k vs. [NaCl] shows a positive slope, whereas when it is absent (*I protein), there is little rate change with salt concentration, as expected for this model.A gp32 variant lacking residues 292-296 within the C-domain, ΔPR201, displays kinetic properties intermediate between gp32 and *I. The single molecule force-induced DNA helix-destabilizing activitiesas well as the single- and double-stranded DNA affinities of ΔPR201 and gp32 truncated at residue 295 also fall between full-length protein and *I. Finally, chemical cross-linking of recombinant C-domain and gp32 lacking both N- and C-terminal domains is inhibited by increasing concentrations of a short single-stranded oligonucleotide, and the salt dependence of cross-linking mirrors that expected for the model. Taken together, these results provide the first evidence in support of this model that have been obtained through structural probes.

Protein-nucleic acid interactions of LINE-1 ORF1p

Long interspersed nuclear element 1 (LINE-1 or L1) is the dominant retrotransposon in mammalian genomes. L1 encodes two proteins ORF1p and ORF2p that are required for retrotransposition. ORF2p functions as the replicase. ORF1p is a coiled coil-mediated trimeric, high affinity RNA binding protein that packages its full- length coding transcript into an ORF2p-containing ribonucleoprotein (RNP) complex, the retrotransposition intermediate. ORF1p also is a nucleic acid chaperone that presumably facilitates the proposed nucleic acid remodeling steps involved in retrotransposition. Although detailed mechanistic understanding of ORF1p function in this process is lacking, recent studies showed that the rate at which ORF1p can form stable nucleic acid-bound oligomers in vitro is positively correlated with formation of an active L1 RNP as assayed in vivo using a cell culture-based retrotransposition assay. This rate was sensitive to minor amino acid changes in the coiled coil domain, which had no effect on nucleic acid chaperone activity. Additional studies linking the complex nucleic acid binding properties to the conformational changes of the protein are needed to understand how ORF1p facilitates retrotransposition.