Poly(ADP-Ribose) glycohydrolase (PARG) vs. poly(ADP-Ribose) polymerase (PARP) – function in genome maintenance and relevance of inhibitors for anti-cancer therapy

Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that catalyze the addition of poly(ADP-ribose) (PAR) subunits onto themselves and other acceptor proteins. PARPs are known to function in a large range of cellular processes including DNA repair, DNA replication, transcription and modulation of chromatin structure. Inhibition of PARP holds great potential for therapy, especially in cancer. Several PARP1/2/3 inhibitors (PARPi) have had success in treating ovarian, breast and prostate tumors harboring defects in the homologous recombination (HR) DNA repair pathway, especially BRCA1/2 mutated tumors. However, treatment is limited to specific sub-groups of patients and resistance can occur, limiting the use of PARPi. Poly(ADP-ribose) glycohydrolase (PARG) reverses the action of PARP enzymes, hydrolysing the ribose-ribose bonds present in poly(ADP-ribose). Like PARPs, PARG is involved in DNA replication and repair and PARG depleted/inhibited cells show increased sensitivity to DNA damaging agents. They also display an accumulation of perturbed replication intermediates which can lead to synthetic lethality in certain contexts. In addition, PARG is thought to play an important role in preventing the accumulation of cytoplasmic PAR and therefore parthanatos, a caspase-independent PAR-mediated type of cell death. In contrast to PARP, the therapeutic potential of PARG has been largely ignored. However, several recent papers have demonstrated the exciting possibilities that inhibitors of this enzyme may have for cancer treatment, both as single agents and in combination with cytotoxic drugs and radiotherapy. This article discusses what is known about the functions of PARP and PARG and the potential future implications of pharmacological inhibition in anti-cancer therapy

Electron correlation energy in confined two-electron systems

Radial, angular and total correlation energies are calculated for four two-electron systems with atomic numbers Z=0-3 confined within an impenetrable sphere of radius R. We report accurate results for the non-relativistic, restricted Hartree-Fock and radial limit energies over a range of confinement radii from 0.05 - 10 a0. At small R, the correlation energies approach limiting values that are independent of Z while at intermediate R, systems with Z > 1 exhibit a characteristic maximum in the correlation energy resulting from an increase in the angular correlation energy which is offset by a decrease in the radial correlation energy

A methodology to compile multi-hazard interrelationships in a data-scarce setting: an application to Kathmandu Valley, Nepal

This paper introduces a multifaceted methodology to identify and compile single natural hazards and multi-hazard interrelationships within the context of data-scarce urban settings, exemplified by Kathmandu Valley, Nepal. This approach integrates (i) five blended types of evidence to support a more nuanced and holistic understanding of a hazardscape where data are scarce and (ii) a 2-hour stakeholder workshop with seven participants to provide greater context to the hazards, consider their impacts through the co-production of multi-hazard interrelationship scenarios, and how this methodology could support more people-centred disaster risk reduction (DRR) strategies. We use blended evidence types, including academic literature, grey literature, media, databases, and social media, to systematically search for exemplars of single hazards and multi-hazard interrelationships that have influenced or could potentially influence Kathmandu Valley. We collated 58 sources of evidence for single hazards and 21 sources of evidence for multi-hazard interrelationships. Using these sources, our study identified 21 single hazard types across six hazard groups (geophysical, hydrological, shallow Earth processes, atmospheric, biophysical, and space/celestial hazards) and 83 multi-hazard interrelationships (12 that have direct case study evidence of previous influence in Kathmandu Valley) that might influence Kathmandu Valley. These exemplars are collated into two databases that accompany this paper. We supplement these exemplars with multi-hazard interrelationship scenarios and multi-hazard impacts developed by stakeholders engaged in DRR research and practice in Kathmandu Valley. The results illustrate the complexity of the hazard landscape, with many single hazards and multi-hazard interrelationships potentially influencing Kathmandu Valley. The research emphasises the importance of inclusive DRR strategies that recognise disaggregated impacts experienced by different social groups. This knowledge can inform the development of dynamic risk scenarios in planning and civil protection, thus strengthening multi-hazard approaches to DRR in “Global South” urban areas such as Kathmandu Valley

Failure regime in (1+1) dimensions in fibrous materials

In this paper, we introduce a model for fracture in fibrous materials that takes into account the rupture height of the fibers, in contrast with previous models. Thus, we obtain the profile of the fracture and calculate its roughness, defined as the variance around the mean height. We investigate the relationship between the fracture roughness and the fracture toughness.Comment: 4 pages, 4 figures.eps, Revte

Synthesis of polyanionic C5-modified 2'-deoxyuridine and 2'-deoxycytidine-5'-triphosphates and their properties as substrates for DNA polymerases

Modified 2'-deoxyribonucleotide triphosphates (dNTPs) have widespread applications in both existing and emerging biomolecular technologies. For such applications it is an essential requirement that the modified dNTPs be substrates for DNA polymerases. To date very few examples of C5-modified dNTPs bearing negatively charged functionality have been described, despite the fact that such nucleotides might potentially be valuable in diagnostic applications using Si-nanowire-based detection systems. Herein we have synthesised C5-modified dUTP and dCTP nucleotides each of which are labelled with an dianionic reporter group. The reporter group is tethered to the nucleobase via a polyethylene glycol (PEG)-based linkers of varying length. The substrate properties of these modified dNTPs with a variety of DNA polymerases have been investigated to study the effects of varying the length and mode of attachment of the PEG linker to the nucleobase. In general, nucleotides containing the PEG linker tethered to the nucleobase via an amide rather than an ether linkage proved to be the best substrates, whilst nucleotides containing PEG linkers from PEG6 to PEG24 could all be incorporated by one or more DNA polymerase. The polymerases most able to incorporate these modified nucleotides included Klentaq, Vent(exo-) and therminator, with incorporation by Klenow(exo-) generally being very poor

Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology

A type of chromosome-free cell called SimCells (simple cells) has been generated from Escherichia coli, Pseudomonas putida, and Ralstonia eutropha. The removal of the native chromosomes of these bacteria was achieved by double-stranded breaks made by heterologous I-CeuI endonuclease and the degradation activity of endogenous nucleases. We have shown that the cellular machinery remained functional in these chromosome-free SimCells and was able to process various genetic circuits. This includes the glycolysis pathway (composed of 10 genes) and inducible genetic circuits. It was found that the glycolysis pathway significantly extended longevity of SimCells due to its ability to regenerate ATP and NADH/NADPH. The SimCells were able to continuously express synthetic genetic circuits for 10 d after chromosome removal. As a proof of principle, we demonstrated that SimCells can be used as a safe agent (as they cannot replicate) for bacterial therapy. SimCells were used to synthesize catechol (a potent anticancer drug) from salicylic acid to inhibit lung, brain, and soft-tissue cancer cells. SimCells represent a simplified synthetic biology chassis that can be programmed to manufacture and deliver products safely without interference from the host genome

Transpacific Transport of Ozone Pollution and the Effect of Recent Asian Emission Increases on Air Quality in North America: An Integrated Analysis Using Satellite, Aircraft, Ozonesonde, and Surface Observations

We use an ensemble of aircraft, satellite, sonde, and surface observations for April–May 2006 (NASA/INTEX-B aircraft campaign) to better understand the mechanisms for transpacific ozone pollution and its implications for North American air quality. The observations are interpreted with a global 3-D chemical transport model (GEOS-Chem). OMI NO2 satellite observations constrain Asian anthropogenic NOx emissions and indicate a factor of 2 increase from 2000 to 2006 in China. Satellite observations of CO from AIRS and TES indicate two major events of Asian transpacific pollution during INTEX-B. Correlation between TES CO and ozone observations shows evidence for transpacific ozone pollution. The semi-permanent Pacific High and Aleutian Low cause splitting of transpacific pollution plumes over the Northeast Pacific. The northern branch circulates around the Aleutian Low and has little impact on North America. The southern branch circulates around the Pacific High and some of that air impacts western North America. Both aircraft measurements and model results show sustained ozone production driven by peroxyacetylnitrate (PAN) decomposition in the southern branch, roughly doubling the transpacific influence from ozone produced in the Asian boundary layer. Model simulation of ozone observations at Mt. Bachelor Observatory in Oregon (2.7 km altitude) indicates a mean Asian ozone pollution contribution of 9±3 ppbv to the mean observed concentration of 54 ppbv, reflecting mostly an enhancement in background ozone rather than episodic Asian plumes. Asian pollution enhanced surface ozone concentrations by 5–7 ppbv over western North America in spring 2006. The 2000–2006 rise in Asian anthropogenic emissions increased this influence by 1–2 ppbv.Earth and Planetary SciencesEngineering and Applied Science

Effects of Impurity Content on the Sintering Characteristics of Plasma-Sprayed Zirconia

Yttria-stabilized zirconia powders, containing different levels of SiO2 and Al2O3, have been plasma sprayed onto metallic substrates. The coatings were detached from their substrates and a dilatometer was used to monitor the dimensional changes they exhibited during prolonged heat treatments. It was found that specimens containing higher levels of silica and alumina exhibited higher rates of linear contraction, in both in-plane and through-thickness directions. The in-plane stiffness and the through-thickness thermal conductivity were also measured after different heat treatments and these were found to increase at a greater rate for specimens with higher impurity (silica and alumina) levels. Changes in the pore architecture during heat treatments were studied using Mercury Intrusion Porosimetry (MIP). Fine scale porosity (<_50 nm) was found to be sharply reduced even by relatively short heat treatments. This is correlated with improvements in inter-splat bonding and partial healing of intra-splat microcracks, which are responsible for the observed changes in stiffness and conductivity, as well as the dimensional changes

Inertial and fluctuational effects on the motion of a Bose superfluid vortex

We study the motion of a vortex under the influence of a harmonic force in an approximately two dimensional trapped Bose-condensed gas. The Hall-Vinen-Iordanskii equations, modified to include a fluctuational force and an inertial mass term, are solved for the vortex motion. The mass of the vortex has a strong influence on the time it takes the vortex to escape the trap. Since the vortex mass also depends on the trap size we have an additional dependence on the trap size in the escape time which we compare to the massless case.Comment: Submitted to J. Low. Temp. Phy

Magnetic Reconnection in Extreme Astrophysical Environments

Magnetic reconnection is a basic plasma process of dramatic rearrangement of magnetic topology, often leading to a violent release of magnetic energy. It is important in magnetic fusion and in space and solar physics --- areas that have so far provided the context for most of reconnection research. Importantly, these environments consist just of electrons and ions and the dissipated energy always stays with the plasma. In contrast, in this paper I introduce a new direction of research, motivated by several important problems in high-energy astrophysics --- reconnection in high energy density (HED) radiative plasmas, where radiation pressure and radiative cooling become dominant factors in the pressure and energy balance. I identify the key processes distinguishing HED reconnection: special-relativistic effects; radiative effects (radiative cooling, radiation pressure, and Compton resistivity); and, at the most extreme end, QED effects, including pair creation. I then discuss the main astrophysical applications --- situations with magnetar-strength fields (exceeding the quantum critical field of about 4 x 10^13 G): giant SGR flares and magnetically-powered central engines and jets of GRBs. Here, magnetic energy density is so high that its dissipation heats the plasma to MeV temperatures. Electron-positron pairs are then copiously produced, making the reconnection layer highly collisional and dressing it in a thick pair coat that traps radiation. The pressure is dominated by radiation and pairs. Yet, radiation diffusion across the layer may be faster than the global Alfv\'en transit time; then, radiative cooling governs the thermodynamics and reconnection becomes a radiative transfer problem, greatly affected by the ultra-strong magnetic field. This overall picture is very different from our traditional picture of reconnection and thus represents a new frontier in reconnection research.Comment: Accepted to Space Science Reviews (special issue on magnetic reconnection). Article is based on an invited review talk at the Yosemite-2010 Workshop on Magnetic Reconnection (Yosemite NP, CA, USA; February 8-12, 2010). 30 pages, no figure