Insights into C4 metabolism from comparative deep sequencing.

C4 photosynthesis suppresses the oxygenation activity of Ribulose Bisphosphate Carboxylase Oxygenase and so limits photorespiration. Although highly complex, it is estimated to have evolved in 66 plant lineages, with the vast majority lacking sequenced genomes. Transcriptomics has recently initiated assessments of the degree to which transcript abundance differs between C3 and C4 leaves, identified novel components of C4 metabolism, and also led to mathematical models explaining the repeated evolution of this complex phenotype. Evidence is accumulating that this complex and convergent phenotype is partly underpinned by parallel evolution of structural genes, but also regulatory elements in both cis and trans. Furthermore, it appears that initial events associated with acquisition of C4 traits likely represent evolutionary exaptations related to non-photosynthetic processes.We thank the BBSRC for grant BB/1002243/1 and the EU 3to4 program for financial support.This is the accepted manuscript. The final version is available at http://www.sciencedirect.com/science/article/pii/S1369526615000680

D-Brane Dynamics and NS5 Rings

We consider the classical motion of a probe D-brane moving in the background geometry of a ring of NS5 branes, assuming that the latter are non-dynamical. We analyse the solutions to the Dirac-Born-Infield (DBI) action governing the approximate dynamics of the system. In the near horizon (throat) approximation we find several exact solutions for the probe brane motion. These are compared to numerical solutions obtained in more general cases. One solution of particular interest is when the probe undergoes oscillatory motion through the centre of the ring (and perpendicular to it). By taking the ring radius sufficiently large, this solution should remain stable to any stringy corrections coming from open-strings stretching between the probe and the NS5-branes along the ring.Comment: 17 pages, Latex, 8 figures; References adde

Atom chips on direct bonded copper substrates

We present the use of direct bonded copper (DBC) for the straightforward fabrication of high power atom chips. Atom chips using DBC have several benefits: excellent copper/substrate adhesion, high purity, thick (> 100 microns) copper layers, high substrate thermal conductivity, high aspect ratio wires, the potential for rapid (< 8 hr) fabrication, and three dimensional atom chip structures. Two mask options for DBC atom chip fabrication are presented, as well as two methods for etching wire patterns into the copper layer. The wire aspect ratio that optimizes the magnetic field gradient as a function of power dissipation is determined to be 0.84:1 (height:width). The optimal wire thickness as a function of magnetic trapping height is also determined. A test chip, able to support 100 A of current for 2 s without failing, is used to determine the thermal impedance of the DBC. An assembly using two DBC atom chips to provide magnetic confinement is also shown.Comment: 8 pages, 5 figure

D-brane dynamics near compactified NS5-branes

We examine the dynamics of a $Dp$-brane in the background of $k$ coincident, parallel $NS$5-branes which have had one of their common transverse directions compactified. We find that for small energy, bound orbits can exist at sufficiently large distances where there will be no stringy effects. The orbits are dependent upon the energy density, angular momentum and electric field. The analysis breaks down at radial distances comparable with the compactification radius and we must resort to using a modified form of the harmonic function in this region.Comment: Latex, 20 pages, 6 figs, references adde

Ancestral light and chloroplast regulation form the foundations for C4 gene expression.

C4 photosynthesis acts as a carbon concentrating mechanism that leads to large increases in photosynthetic efficiency. The C4 pathway is found in more than 60 plant lineages1 but the molecular enablers of this evolution are poorly understood. In particular, it is unclear how non-photosynthetic proteins in the ancestral C3 system have repeatedly become strongly expressed and integrated into photosynthesis gene regulatory networks in C4 leaves. Here, we provide clear evidence that in C3 leaves, genes encoding key enzymes of the C4 pathway are already co-regulated with photosynthesis genes and are controlled by both light and chloroplast-to-nucleus signalling. In C4 leaves this regulation becomes increasingly dependent on the chloroplast. We propose that regulation of C4 cycle genes by light and the chloroplast in the ancestral C3 state has facilitated the repeated evolution of the complex and convergent C4 trait.The work was funded by the European Union 3to4 project and Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/J011754/1. I.G.-M. was supported by the Amgen Foundation. Research on chloroplast signalling by M.J.T. was supported by BBSRC grant (BB/J018139/1).This is the author accepted manuscript. The final version is available from the Nature Publishing Group via http://dx.doi.org/10.1038/nplants.2016.16

Shared characteristics underpinning C 4 leaf maturation derived from analysis of multiple C 3 and C 4 species of Flaveria

Most terrestrial plants use C3 photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4 photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4 photosynthesis, the genus Flaveria that contains C3 and C4 species was used. A base to tip maturation gradient of leaf anatomy was defined, and RNA sequencing was undertaken along this gradient for two C3 and two C4Flaveria species. Key C4 traits including vein density, mesophyll and bundle sheath cross-sectional area, chloroplast ultrastructure, and abundance of transcripts encoding proteins of C4 photosynthesis were quantified. Candidate genes underlying each of these C4 characteristics were identified. Principal components analysis indicated that leaf maturation and the photosynthetic pathway were responsible for the greatest amount of variation in transcript abundance. Photosynthesis genes were over-represented for a prolonged period in the C4 species. Through comparison with publicly available data sets, we identify a small number of transcriptional regulators that have been up-regulated in diverse C4 species. The analysis identifies similar patterns of expression in independent C4 lineages and so indicates that the complex C4 pathway is associated with parallel as well as convergent evolution

Finite sampling interval effects in Kramers-Moyal analysis

Large sampling intervals can affect reconstruction of Kramers-Moyal coefficients from data. A new method, which is direct, non-stochastic and exact up to numerical accuracy, can estimate these finite-time effects. For the first time, exact finite-time effects are described analytically for special cases; biologically inspired numerical examples are also worked through numerically. The approach developed here will permit better evaluation of Langevin or Fokker-Planck based models from data with large sampling intervals. It can also be used to predict the sampling intervals for which finite-time effects become significant.Comment: Preprin