Nucleon-Nucleon Optical Model for Energies to 3 GeV

Several nucleon-nucleon potentials, Paris, Nijmegen, Argonne, and those derived by quantum inversion, which describe the NN interaction for T-lab below 300$ MeV are extended in their range of application as NN optical models. Extensions are made in r-space using complex separable potentials definable with a wide range of form factor options including those of boundary condition models. We use the latest phase shift analyses SP00 (FA00, WI00) of Arndt et al. from 300 MeV to 3 GeV to determine these extensions. The imaginary parts of the optical model interactions account for loss of flux into direct or resonant production processes. The optical potential approach is of particular value as it permits one to visualize fusion, and subsequent fission, of nucleons when T-lab above 2 GeV. We do so by calculating the scattering wave functions to specify the energy and radial dependences of flux losses and of probability distributions. Furthermore, half-off the energy shell t-matrices are presented as they are readily deduced with this approach. Such t-matrices are required for studies of few- and many-body nuclear reactions.Comment: Latex, 40 postscript pages including 17 figure

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world's potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments

Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

Genomic selection can increase genetic gain per generation through early selection. Genomic selection is expected to be particularly valuable for traits that are costly to phenotype and expressed late in the life cycle of long-lived species. Alternative approaches to genomic selection prediction models may perform differently for traits with distinct genetic properties. Here the performance of four different original methods of genomic selection that differ with respect to assumptions regarding distribution of marker effects, including (i) ridge regression–best linear unbiased prediction (RR–BLUP), (ii) Bayes A, (iii) Bayes Cπ, and (iv) Bayesian LASSO are presented. In addition, a modified RR–BLUP (RR–BLUP B) that utilizes a selected subset of markers was evaluated. The accuracy of these methods was compared across 17 traits with distinct heritabilities and genetic architectures, including growth, development, and disease-resistance properties, measured in a Pinus taeda (loblolly pine) training population of 951 individuals genotyped with 4853 SNPs. The predictive ability of the methods was evaluated using a 10-fold, cross-validation approach, and differed only marginally for most method/trait combinations. Interestingly, for fusiform rust disease-resistance traits, Bayes Cπ, Bayes A, and RR–BLUB B had higher predictive ability than RR–BLUP and Bayesian LASSO. Fusiform rust is controlled by few genes of large effect. A limitation of RR–BLUP is the assumption of equal contribution of all markers to the observed variation. However, RR-BLUP B performed equally well as the Bayesian approaches.The genotypic and phenotypic data used in this study are publically available for comparative analysis of genomic selection prediction models

WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids

Self-organization of discrete fates in human gastruloids is mediated by a hierarchy of signaling pathways. How these pathways are integrated in time, and whether cells maintain a memory of their signaling history remains obscure. Here, we dissect the temporal integration of two key pathways, WNT and ACTIVIN, which along with BMP control gastrulation. CRISPR/Cas9-engineered live reporters of SMAD1, 2 and 4 demonstrate that in contrast to the stable signaling by SMAD1, signaling and transcriptional response by SMAD2 is transient, and while necessary for pluripotency, it is insufficient for differentiation. Pre-exposure to WNT, however, endows cells with the competence to respond to graded levels of ACTIVIN, which induces differentiation without changing SMAD2 dynamics. This cellular memory of WNT signaling is necessary for ACTIVIN morphogen activity. A re-evaluation of the evidence gathered over decades in model systems, re-enforces our conclusions and points to an evolutionarily conserved mechanism

SN 2009md: Another faint supernova from a low mass progenitor

We present adaptive optics imaging of the core collapse supernova (SN) 2009md, which we use together with archival \emph{Hubble Space Telescope} data to identify a coincident progenitor candidate. We find the progenitor to have an absolute magnitude of $V = -4.63^{+0.3}_{-0.4}$ mag and a colour of $V-I = 2.29^{+0.25}_{-0.39}$ mag, corresponding to a progenitor luminosity of log $L$/L$_{\odot}$ $\sim4.54\pm0.19$ dex. Using the stellar evolution code STARS, we find this to be consistent with a red supergiant progenitor with $M = 8.5_{-1.5}^{+6.5}$ M$_{\odot}$. The photometric and spectroscopic evolution of SN 2009md is similar to that of the class of sub-luminous Type IIP SNe; in this paper we compare the evolution of SN 2009md primarily to that of the sub-luminous SN 2005cs. We estimate the mass of $^{56}$Ni ejected in the explosion to be $(5.4\pm1.3) \times 10^{-3}$ M$_{\odot}$\ from the luminosity on the radioactive tail, which is in agreement with the low $^{56}$Ni masses estimated for other sub-luminous Type IIP SNe. From the lightcurve and spectra, we show the SN explosion had a lower energy and ejecta mass than the normal Type IIP SN 1999em. We discuss problems with stellar evolutionary models, and the discrepancy between low observed progenitor luminosities (log $L$/L$_{\odot}$ $\sim4.3-5$ dex) and model luminosities after the second-dredge-up for stars in this mass range, and consider an enhanced carbon burning rate as a possible solution. In conclusion, SN 2009md is a faint SN arising from the collapse of a progenitor close to the lower mass limit for core-collapse. This is now the third discovery of a low mass progenitor star producing a low energy explosion and low $^{56}$Ni ejected mass, which indicates that such events arise from the lowest end of the mass range that produces a core-collapse supernova (7-8 M$_{\odot}$).Comment: MNRAS accepted, revised version following referee's comment