Nuclear weapons fallout 137Cs in temperate and tropical pine forest soils, 50 years post-deposition

Following nuclear releases to the environment, 137Cs (half-life 30 years) is a long-term contaminant of many ecosystems, including forests. We recently sampled soils under pine forests in temperate and tropical climates to test the hypothesis that migration of 137Cs, 50 years after nuclear weapons fallout, is coupled with organic matter (OM) accumulation in these soils. Depth profiles of 137Cs, naturally-occurring 210Pb and weapons-derived 241Am were measured. After 50 years, migration of 137Cs into the temperate and tropical soils is limited to half-depths of 7–8 cm and 2–3 cm, respectively. At both locations, most 137Cs is associated with OM that accumulated from the early to mid-1960s. Illite, which immobilises radiocaesium, was undetectable by X-ray diffraction in the layer of peak 137Cs accumulation in the temperate forest soil, but apparent in the zone of peak concentration in the tropical soil. Data indicate that long-term (50 year) fate of 137Cs in organic-rich, temperate forest soil is coupled with OM accumulation; fixation of 137Cs by illite is more important in the tropical forest soil where OM is rapidly decomposed. Models of long-term radiocaesium migration in forest soils should explicitly account for the role of OM, especially when considering forests under contrasting climatic regimes

Clostridium difficile surface proteins are anchored to the cell wall using CWB2 motifs that recognise the anionic polymer PSII

Gram-positive surface proteins can be covalently or non-covalently anchored to the cell wall and can impart important properties on the bacterium in respect of cell envelope organisation and interaction with the environment. We describe here a mechanism of protein anchoring involving tandem CWB2 motifs found in a large number of cell wall proteins in the Firmicutes. In the Clostridium difficile cell wall protein family, we show the three tandem repeats of the CWB2 motif are essential for correct anchoring to the cell wall. CWB2 repeats are non-identical and cannot substitute for each other, as shown by the secretion into the culture supernatant of proteins containing variations in the patterns of repeats. A conserved Ile Leu Leu sequence within the CWB2 repeats is essential for correct anchoring, although a preceding proline residue is dispensable. We propose a likely genetic locus encoding synthesis of the anionic polymer PSII and, using RNA knock-down of key genes, reveal subtle effects on cell wall composition. We show that the anionic polymer PSII binds two cell wall proteins, SlpA and Cwp2, and these interactions require the CWB2 repeats, defining a new mechanism of protein anchoring in Gram-positive bacteria

Phosphate steering by Flap Endonuclease 1 promotes 5´-flap specificity and incision to prevent genome instability

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 50-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 50-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 50polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via ‘phosphate steering’, basic residues energetically steer an inverted ss 50-flap through a gateway over FEN1’s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA)n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 50-flap specificity and catalysis, preventing genomic instability

Phosphate steering by Flap Endonuclease 1 promotes 5´-flap specificity and incision to prevent genome instability

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 50-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 50-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 50polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via ‘phosphate steering’, basic residues energetically steer an inverted ss 50-flap through a gateway over FEN1’s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA)n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 50-flap specificity and catalysis, preventing genomic instability

Edge effects in a frustrated Josephson junction array with modulated couplings

A square array of Josephson junctions with modulated strength in a magnetic field with half a flux quantum per plaquette is studied by analytic arguments and dynamical simulations. The modulation is such that alternate columns of junctions are of different strength to the rest. Previous work has shown that this system undergoes an XY followed by an Ising-like vortex lattice disordering transition at a lower temperature. We argue that resistance measurements are a possible probe of the vortex lattice disordering transition as the linear resistance $R_{L}(T)\sim A(T)/L$ with $A(T) \propto (T-T_{cI})$ at intermediate temperatures $T_{cXY}>T>T_{cI}$ due to dissipation at the array edges for a particular geometry and vanishes for other geometries. Extensive dynamical simulations are performed which support the qualitative physical arguments.Comment: 8 pages with figs, RevTeX, to appear in Phys. Rev.

Multi-parameter Entanglement in Quantum Interferometry

The role of multi-parameter entanglement in quantum interference from collinear type-II spontaneous parametric down-conversion is explored using a variety of aperture shapes and sizes, in regimes of both ultrafast and continuous-wave pumping. We have developed and experimentally verified a theory of down-conversion which considers a quantum state that can be concurrently entangled in frequency, wavevector, and polarization. In particular, we demonstrate deviations from the familiar triangular interference dip, such as asymmetry and peaking. These findings improve our capacity to control the quantum state produced by spontaneous parametric down-conversion, and should prove useful to those pursuing the many proposed applications of down-converted light.Comment: submitted to Physical Review

NMR and NQR Fluctuation Effects in Layered Superconductors

We study the effect of thermal fluctuations of the s-wave order parameter of a quasi two dimensional superconductor on the nuclear spin relaxation rate near the transition temperature Tc. We consider both the effects of the amplitude fluctuations and the Berezinskii-Kosterlitz-Thouless (BKT) phase fluctuations in weakly coupled layered superconductors. In the treatment of the amplitude fluctuations we employ the Gaussian approximation and evaluate the longitudinal relaxation rate 1/T1 for a clean s-wave superconductor, with and without pair breaking effects, using the static pair fluctuation propagator D. The increase in 1/T1 due to pair breaking in D is overcompensated by the decrease arising from the single particle Green's functions. The result is a strong effect on 1/T1 for even a small amount of pair breaking. The phase fluctuations are described in terms of dynamical BKT excitations in the form of pancake vortex-antivortex (VA) pairs. We calculate the effect of the magnetic field fluctuations caused by the translational motion of VA excitations on 1/T1 and on the transverse relaxation rate 1/T2 on both sides of the BKT transitation temperature T(BKT)<Tc. The results for the NQR relaxation rates depend strongly on the diffusion constant that governs the motion of free and bound vortices as well as the annihilation of VA pairs. We discuss the relaxation rates for real multilayer systems where the diffusion constant can be small and thus increase the lifetime of a VA pair, leading to an enhancement of the rates. We also discuss in some detail the experimental feasibility of observing the effects of amplitude fluctuations in layered s-wave superconductors such as the dichalcogenides and the effects of phase fluctuations in s- or d-wave superconductors such as the layered cuprates.Comment: 38 pages, 12 figure

Entangled-Photon Generation from Parametric Down-Conversion in Media with Inhomogeneous Nonlinearity

We develop and experimentally verify a theory of Type-II spontaneous parametric down-conversion (SPDC) in media with inhomogeneous distributions of second-order nonlinearity. As a special case, we explore interference effects from SPDC generated in a cascade of two bulk crystals separated by an air gap. The polarization quantum-interference pattern is found to vary strongly with the spacing between the two crystals. This is found to be a cooperative effect due to two mechanisms: the chromatic dispersion of the medium separating the crystals and spatiotemporal effects which arise from the inclusion of transverse wave vectors. These effects provide two concomitant avenues for controlling the quantum state generated in SPDC. We expect these results to be of interest for the development of quantum technologies and the generation of SPDC in periodically varying nonlinear materials.Comment: submitted to Physical Review

Long term follow up of persistence of immunity following quadrivalent Human Papillomavirus (HPV) vaccine in immunocompromised children

Background: Human Papillomavirus (HPV) causes significant burden of HPV-related diseases, which are more prevalent in immunosuppressed compared to immunocompetent people. We conducted a multi-centre clinical trial to determine the immunogenicity and reactogenicity of HPV vaccine in immunocompromised children. Here we present the immunogenicity results 5 years post vaccination. Methods: We followed up immunocompromised children (5-18 years) with a range of specified underlying conditions who were previously recruited from three Australian paediatric hospitals. Participants received three doses of quadrivalent HPV vaccine (Gardasil Quadrivalent HPV Types 6, 11, 16, 18) and were followed up between 2007 and 2016 (60 months post-vaccination). The immunogenicity primary outcome was seroconversion and geometric mean titres (GMT) of the quadrivalent HPV vaccine serotypes in the study. Results: Of the 59 original participants, 37 were followed up at 60 months. The proportion of participants who seroconverted were: 86.5%, 89.2%, 89.2%, 91.9% by competitive Luminex immunoassay (cLIA) and 83.8%, 83.8%, 94.6%, 78.4% by total immunoglobulin G assays (IgG) for serotypes 6, 11, 16 and 18 respectively. GMT values ranged from 118 (95%CI: 79-177) for serotype 11, to 373 (95%CI: 215-649) for serotype 16 by cLIA. For IgG, serotype 16 had the highest GMT of 261 (95%CI: 143-477) and serotype 18 had the lowest value of 37 (95%CI: 21-68). All antibody titres were lower in females compared to males but the difference was not statistically significant except for serotype 16. No serious adverse event was reported during this follow-up period. Conclusion: Our evidence, although limited by small numbers, is reassuring that a three dose schedule of HPV vaccine remains immunogenic in immunocompromised children to five years post vaccination. Large scale studies are required to determine long term protection in immunocompromised children.C. Raina MacIntyre, Peter J. Shaw, Fiona E. Mackie, Christina Boros, Helen Marshall, Holly Seale, Sean E. Kennedy, Aye Moa, Abrar Ahmad Chughtai, Mallory Trent, Edward V O’Loughlin, Michael Stormo