Structure of SPH (Self-Incompatibility Protein Homologue) Proteins: a Widespread Family of Small, Highly Stable, Secreted Proteins

SPH proteins are a large family of small, disulphide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy , but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of , we expressed one member of this family, SPH15 from , as a folded thioredoxin-fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism, and NMR spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a beta-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins; human transthyretin, bacterial TSSJ, and pneumolysin, with no discernable sequence similarity. The NMR-derived structure was compared with a model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from , which have only 15-18% sequence homology to SPH15. The DeepCDPred method gave models with lower Discreet Optimised Protein Energy (DOPE) scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes. [Abstract copyright: ©2019 The Author(s).

Wear and biological effects of a semi-constrained total disc replacement subject to modified ISO standard test conditions

Development of pre-clinical testing methodologies is an important goal for improving prediction of artificial replacement joint performance and for guiding future device design. Total disc replacement wear and the potential for osteolysis is a growing concern, therefore a parametric study on the effects on wear of altered kinematics and loading was undertaken. A standard ISO testing protocol was modified in order to study the wear behaviour of lumbar total disc replacements when subject to low cross shear input kinematics, reduced axial loading and smaller flexion–extension magnitude. Volumetric wear, bearing surface topography, and wear debris biological reactivity were assessed. The ISO standard results were expected, however, the very low cross shear test produced a level of wear approximately two orders of magnitude higher than that reported for zero cross shear motions on UHMWPE bearings. When the osteolytic potential of the wear particles was calculated, all total disc replacement simulations had lower predicted osteolytic potential compared to total hip replacements, as a consequence of the generally lower wear rates found

Quasielastic 12C(e,e'p) Reaction at High Momentum Transfer

We measured the 12C(e,e'p) cross section as a function of missing energy in parallel kinematics for (q,w) = (970 MeV/c, 330 MeV) and (990 MeV/c, 475 MeV). At w=475 MeV, at the maximum of the quasielastic peak, there is a large continuum (E_m > 50 MeV) cross section extending out to the deepest missing energy measured, amounting to almost 50% of the measured cross section. The ratio of data to DWIA calculation is 0.4 for both the p- and s-shells. At w=330 MeV, well below the maximum of the quasielastic peak, the continuum cross section is much smaller and the ratio of data to DWIA calculation is 0.85 for the p-shell and 1.0 for the s-shell. We infer that one or more mechanisms that increase with $\omega$ transform some of the single-nucleon-knockout into multinucleon knockout, decreasing the valence knockout cross section and increasing the continuum cross section.Comment: 14 pages, 7 figures, Revtex (multicol, prc and aps styles), to appear in Phys Rev

Reducing nitrous oxide emissions by changing N fertiliser use from calcium ammonium nitrate (CAN) to urea based formulations

This research was financially supported under the National Development Plan, through the Research Stimulus Fund, administered by the Department of Agriculture, Food and the Marine (Grant numbers RSF10-/RD/SC/716 and RSF11S138) and from the Department of Agriculture and Rural Development (Ref: DARD Evidence and Innovation project 13/04/06) for Northern Ireland. The first author gratefully acknowledges funding received from the Teagasc Walsh Fellowship Scheme (Ref: 2012005).peer-reviewedThe accelerating use of synthetic nitrogen (N) fertilisers, to meet the world's growing food demand, is the primary driver for increased atmospheric concentrations of nitrous oxide (N2O). The IPCC default emission factor (EF) for N2O from soils is 1% of the N applied, irrespective of its form. However, N2O emissions tend to be higher from nitrate-containing fertilisers e.g. calcium ammonium nitrate (CAN) compared to urea, particularly in regions, which have mild, wet climates and high organic matter soils. Urea can be an inefficient N source due to NH3 volatilisation, but nitrogen stabilisers (urease and nitrification inhibitors) can improve its efficacy. This study evaluated the impact of switching fertiliser formulation from calcium ammonium nitrate (CAN) to urea-based products, as a potential mitigation strategy to reduce N2O emissions at six temperate grassland sites on the island of Ireland. The surface applied formulations included CAN, urea and urea with the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) and/or the nitrification inhibitor dicyandiamide (DCD). Results showed that N2O emissions were significantly affected by fertiliser formulation, soil type and climatic conditions. The direct N2O emission factor (EF) from CAN averaged 1.49% overall sites, but was highly variable, ranging from 0.58% to 3.81. Amending urea with NBPT, to reduce ammonia volatilisation, resulted in an average EF of 0.40% (ranging from 0.21 to 0.69%)-compared to an average EF of 0.25% for urea (ranging from 0.1 to 0.49%), with both fertilisers significantly lower and less variable than CAN. Cumulative N2O emissions from urea amended with both NBPT and DCD were not significantly different from background levels. Switching from CAN to stabilised urea formulations was found to be an effective strategy to reduce N2O emissions, particularly in wet, temperate grassland.Department of Agriculture and Rural Development for Northern IrelandTeagasc Walsh Fellowship ProgrammeDepartment of Agriculture, Food and the Marin

Population connectivity of the highly migratory shortfin mako (Isurus oxyrinchus Rafinesque 1810) and implications for management in the Southern Hemisphere

Published: 20 November 2018In this paper we combine analyses of satellite telemetry and molecular data to investigate spatial connectivity and genetic structure among populations of shortfin mako (Isurus oxyrinchus) in and around Australian waters, where this species is taken in recreational and commercial fisheries. Mitochondrial DNA data suggest matrilineal substructure across hemispheres, while nuclear DNA data indicate shortfin mako may constitute a globally panmictic population. There was generally high genetic connectivity within Australian waters. Assessing genetic connectivity across the Indian Ocean basin, as well as the extent that shortfin mako exhibit sex biases in dispersal patterns would benefit from future improved sampling of adult size classes, particularly of individuals from the eastern Indian Ocean. Telemetry data indicated that Australasian mako are indeed highly migratory and frequently make long-distance movements. However, individuals also exhibit fidelity to relatively small geographic areas for extended periods. Together these patterns suggest that shortfin mako populations may be genetically homogenous across large geographical areas as a consequence of few reproductively active migrants, although spatial partitioning exists. Given that connectivity appears to occur at different scales, management at both the national and regional levels seems most appropriate.Shannon Corrigan, Andrew D. Lowther, Luciano B. Beheregaray, Barry D. Bruce, Geremy Cliff, Clinton A. Duffy, Alan Foulis, Malcolm P. Francis, Simon D. Goldsworthy, John R. Hyde, Rima W. Jabado, Dovi Kacev, Lindsay Marshall, Gonzalo R. Mucientes, Gavin J. P. Naylor, Julian G. Pepperell, Nuno Queiroz, William T. White, Sabine P. Wintner and Paul J. Roger

Early carboniferous brachiopod faunas from the Baoshan block, west Yunnan, southwest China

38 brachiopod species in 27 genera and subgenera are described from the Yudong Formation in the Shidian-Baoshan area, west Yunnan, southwest China. New taxa include two new subgenera: Unispirifer (Septimispirifer) and Brachythyrina (Longathyrina), and seven new species: Eomarginifera yunnanensis, Marginatia cylindrica, Unispirifer (Unispirifer) xiangshanensis, Unispirifer (Septimispirifer) wafangjieensis, Brachythyrina (Brachythyrina) transversa, Brachythyrina (Longathyrina) baoshanensis, and Girtyella wafangjieensis. Based on the described material and constraints from associated coral and conodont faunas, the age of the brachiopod fauna from the Yudon Formation is considered late Tournaisian (Early Carboniferous), with a possibility extending into earlyViseacutean.<br /

Prospects for e+e- physics at Frascati between the phi and the psi

We present a detailed study, done in the framework of the INFN 2006 Roadmap, of the prospects for e+e- physics at the Frascati National Laboratories. The physics case for an e+e- collider running at high luminosity at the phi resonance energy and also reaching a maximum center of mass energy of 2.5 GeV is discussed, together with the specific aspects of a very high luminosity tau-charm factory. Subjects connected to Kaon decay physics are not discussed here, being part of another INFN Roadmap working group. The significance of the project and the impact on INFN are also discussed. All the documentation related to the activities of the working group can be found in http://www.roma1.infn.it/people/bini/roadmap.html.Comment: INFN Roadmap Report: 86 pages, 25 figures, 9 table

Search for gravitational waves from Scorpius X-1 in the second Advanced LIGO observing run with an improved hidden Markov model

We present results from a semicoherent search for continuous gravitational waves from the low-mass x-ray binary Scorpius X-1, using a hidden Markov model (HMM) to track spin wandering. This search improves on previous HMM-based searches of LIGO data by using an improved frequency domain matched filter, the J-statistic, and by analyzing data from Advanced LIGO's second observing run. In the frequency range searched, from 60 to 650 Hz, we find no evidence of gravitational radiation. At 194.6 Hz, the most sensitive search frequency, we report an upper limit on gravitational wave strain (at 95% confidence) of h095%=3.47×10-25 when marginalizing over source inclination angle. This is the most sensitive search for Scorpius X-1, to date, that is specifically designed to be robust in the presence of spin wandering. © 2019 American Physical Society

Erratum: "A Gravitational-wave Measurement of the Hubble Constant Following the Second Observing Run of Advanced LIGO and Virgo" (2021, ApJ, 909, 218)

[no abstract available

Search for Tensor, Vector, and Scalar Polarizations in the Stochastic Gravitational-Wave Background

The detection of gravitational waves with Advanced LIGO and Advanced Virgo has enabled novel tests of general relativity, including direct study of the polarization of gravitational waves. While general relativity allows for only two tensor gravitational-wave polarizations, general metric theories can additionally predict two vector and two scalar polarizations. The polarization of gravitational waves is encoded in the spectral shape of the stochastic gravitational-wave background, formed by the superposition of cosmological and individually unresolved astrophysical sources. Using data recorded by Advanced LIGO during its first observing run, we search for a stochastic background of generically polarized gravitational waves. We find no evidence for a background of any polarization, and place the first direct bounds on the contributions of vector and scalar polarizations to the stochastic background. Under log-uniform priors for the energy in each polarization, we limit the energy densities of tensor, vector, and scalar modes at 95% credibility to Ω0T<5.58×10-8, Ω0V<6.35×10-8, and Ω0S<1.08×10-7 at a reference frequency f0=25 Hz. © 2018 American Physical Society