DNA Charge Transport: from Chemical Principles to the Cell

The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology

Multiplexed Electrochemistry of DNA-Bound Metalloproteins

Here we describe a multiplexed electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins containing redox cofactors, and multiplexing offers a means to probe different complex samples and substrates in parallel to elucidate this chemistry. Multiplexed analysis of endonuclease III (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, shows subtle differences in the electrochemical behavior as a function of DNA morphology. The peak splitting, signal broadness, sensitivity to π-stack perturbations, and kinetics were all characterized for the DNA-bound reduction of EndoIII on both closely and loosely packed DNA films. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction; closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. Multiplexing furthermore permits the comparison of the electrochemistry of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster

DNA Protection by the Bacterial Ferritin Dps via DNA Charge Transport

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. Here we examine the mechanism of E. coli Dps protection of DNA, specifically whether this DNA-binding protein can utilize DNA charge transport through the base pair π-stack to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate DNA damage localized to guanine repeats, the sites of lowest potential in DNA. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps, significantly attenuates the yield of oxidative DNA damage. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA charge transport may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance

The prevalence and causes of vision loss in Indigenous Australians: the National Indigenous Eye Health Survey

Aim: To determine the prevalence and causes of vision loss in Indigenous Australians. Design, setting and participants: A national, stratified, random cluster sample was drawn from 30 communities across Australia that each included about 300 Indigenous people of all ages. A sample of non-Indigenous adults aged 40 years was also tested at several remote sites for comparison. Participants were examined using a standardised protocol that included a questionnaire (self-administered or completed with the help of field staff), visual acuity (VA) testing on presentation and after correction, visual field testing, trachoma grading, and fundus and lens photography. The data were collected in 2008. Main outcome measures: VA; prevalence of low vision and blindness; causes of vision loss; rates of vision loss in Indigenous compared with non-Indigenous adults. Results: 1694Indigenouschildrenand1189Indigenousadultswereexamined, representing recruitment rates of 84% for children aged 5–15 years and 72% for adults aged 40 years. Rates of low vision (VA \u3c 6/12 to 6/60) were 1.5% (95% CI, 0.9%–2.1%) in children and 9.4% (95% CI, 7.8%–11.1%) in adults. Rates of blindness (VA \u3c 6/60) were 0.2% (95% CI, 0.04%–0.5%) in children and 1.9% (95% CI, 1.1%–2.6%) in adults. The principal cause of low vision in both adults and children was refractive error. The principal causes of blindness in adults were cataract, refractive error and optic atrophy. Relative risks (RRs) of vision loss and blindness in Indigenous adults compared with adults in the mainstream Australian population were 2.8 and 6.2, respectively. By contrast, RRs of vision loss and blindness in Indigenous children compared with mainstream children were 0.2 and 0.6, respectively. Conclusion: Many causes of vision loss in our sample were readily avoidable. Better allocation of services and resources is required to give all Australians equal access to eye health services

Energy expenditure and body temperature variations in llamas living in the High Andes of Peru

The authors thank Emma Quina and Yurguen Peña for organising the field trips and for technical help and two anonymous reviewers for their help improving the manuscript. The study was supported by a research grant from the German Research Foundation (DFG) to A.R. (RI 1796/3-1). The data analysed during the current study are available from the corresponding author on reasonable request.Peer reviewedPublisher PD

Quasiparticle Description of the QCD Plasma, Comparison with Lattice Results at Finite T and Mu

We compare our 2+1 flavor, staggered QCD lattice results with a quasiparticle picture. We determine the pressure, the energy density, the baryon density, the speed of sound and the thermal masses as a function of T and $\mu_B$. For the available thermodynamic quantities the difference is a few percent between the results of the two approaches. We also give the phase diagram on the $\mu_B$--T plane and estimate the critical chemical potential at vanishing temperature.Comment: 13 pages, 10 figure

Sulfur K-Edge XAS Studies of the Effect of DNA Binding on the [Fe_4S_4] Site in EndoIII and MutY

S K-edge X-ray absorption spectroscopy (XAS) was used to study the [Fe_4S_4] clusters in the DNA repair glycosylases EndoIII and MutY to evaluate the effects of DNA binding and solvation on Fe–S bond covalencies (i.e., the amount of S 3p character mixed into the Fe 3d valence orbitals). Increased covalencies in both iron–thiolate and iron–sulfide bonds would stabilize the oxidized state of the [Fe_4S_4] clusters. The results are compared to those on previously studied [Fe_4S_4] model complexes, ferredoxin (Fd), and to new data on high-potential iron–sulfur protein (HiPIP). A limited decrease in covalency is observed upon removal of solvent water from EndoIII and MutY, opposite to the significant increase observed for Fd, where the [Fe_4S_4] cluster is solvent exposed. Importantly, in EndoIII and MutY, a large increase in covalency is observed upon DNA binding, which is due to the effect of its negative charge on the iron–sulfur bonds. In EndoIII, this change in covalency can be quantified and makes a significant contribution to the observed decrease in reduction potential found experimentally in DNA repair proteins, enabling their HiPIP-like redox behavior

Epidemiology of pleural empyema in English hospitals and the impact of influenza

Pleural empyema represents a significant healthcare burden due to extended hospital admissions and potential requirement for surgical intervention. This study aimed to assess changes in incidence and management of pleural empyema in England over the past 10 years and the potential impact of influenza on rates. Hospital Episode Statistics data were used to identify patients admitted to English hospitals with pleural empyema between 2008 and 2018. Linear regression was used to analyse the relationship between empyema rates and influenza incidence recorded by Public Health England. The relationship between influenza and empyema was further explored using serological data from a prospective cohort study of patients presenting with pleural empyema. Between April 2008 and March 2018 there were 55 530 patients admitted with pleural empyema. There was male predominance (67% versus 33%), which increased with age. Cases have increased significantly from 4447 in 2008 to 7268 in 2017. Peaks of incidence correlated moderately with rates of laboratoryconfirmed influenza in children and young adults (r=0.30). For nine of the 10 years studied, the highest annual point incidence of influenza coincided with the highest admission rate for empyema (with a 2-week lag). In a cohort study of patients presenting to a single UK hospital with pleural empyema/ infection, 24% (17 out of 72) had serological evidence of recent influenza infection, compared to 7% in seasonally matched controls with simple parapneumonic or cardiogenic effusions (p<0.001). Rates of empyema admissions in England have increased steadily with a seasonal variation that is temporally related to influenza incidence. Patient-level serological data from a prospective study support the hypothesis that influenza may play a pathogenic role in empyema development

Insights into the influence of solvent polarity on the crystallization of poly(ethylene oxide) spin-coated thin films via in situ grazing incidence wide-angle X-ray scattering

Controlling polymer thin-film morphology and crystallinity is crucial for a wide range of applications, particularly in thin-film organic electronic devices. In this work, the crystallization behavior of a model polymer, poly(ethylene oxide) (PEO), during spin-coating is studied. PEO films were spun-cast from solvents possessing different polarities (chloroform, THF, and methanol) and probed via in situ grazing incidence wide-angle X-ray scattering. The crystallization behavior was found to follow the solvent polarity order (where chloroform chloroform > methanol). When spun-cast from nonpolar chloroform, crystallization largely followed Avrami kinetics, resulting in the formation of morphologies comprising large spherulites. PEO solutions cast from more polar solvents (THF and methanol) do not form well-defined highly crystalline morphologies and are largely amorphous with the presence of small crystalline regions. The difference in morphological development of PEO spun-cast from polar solvents is attributed to clustering phenomena that inhibit polymer crystallization. This work highlights the importance of considering individual components of polymer solubility, rather than simple total solubility, when designing processing routes for the generation of morphologies with optimum crystallinities or morphologies