Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom

International audienceEukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Crypto-coccus yeast species by genome-wide mapping of translation and of mRNA 5 and 3 ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Crypto-coccus mRNAs encode predicted dual-localized proteins , including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi

The Mount Perkins block, northwestern Arizona: An exposed cross section of an evolving, preextensional to synextensional magmatic system

This is the published version. Reuse is subject to Society of Exploration Geophysicists terms of use and conditions.The steeply tilted Mount Perkins block, northwestern Arizona, exposes a cross section of a magmatic system that evolved through the onset of regional extension. New 40Ar/39Ar ages of variably tilted (0–90°) volcanic strata bracket extension between 15.7 and 11.3 Ma. Preextensional intrusive activity included emplacement of a composite Miocene laccolith and stock, trachydacite dome complex, and east striking rhyolite dikes. Related volcanic activity produced an ∼18–16 Ma stratovolcano, cored by trachydacite domes and flanked by trachydacite-trachyandesite flows, and ∼16 Ma rhyolite flows. Similar compositions indicate a genetic link between the stratovolcano and granodioritic phase of the laccolith. Magmatic activity synchronous with early regional extension (15.7–14.5 Ma) generated a thick, felsic volcanic sequence, a swarm of northerly striking subvertical rhyolite dikes, and rhyolite domes. Field relations and compositions indicate that the dike swarm and felsic volcanic sequence are cogenetic. Modes of magma emplacement changed during the onset of extension from subhorizontal sheets, east striking dikes, and stocks to northerly striking, subvertical dike swarms, as the regional stress field shifted from nearly isotropic to decidedly anisotropic with an east-west trending, horizontal least principal stress. Preextensional trachydacitic and preextensional to synextensional rhyolitic magmas were part of an evolving system, which involved the ponding of mantle-derived basaltic magmas and ensuing crustal melting and assimilation at progressively shallower levels. Major extension halted this system by generating abundant pathways to the surface (fractures), which flushed out preexisting crustal melts and hybrid magmas. Remaining silicic melts were quenched by rapid, upper crustal cooling induced by tectonic denudation. These processes facilitated eruption of mafic magmas. Accordingly, silicic magmatism at Mount Perkins ended abruptly during peak extension ∼14.5 Ma and gave way to mafic magmatism, which continued until extension ceased

A Search for Sigma^0_5, N^0_5 and Theta^++ Pentaquark States

A high-resolution (sigma_instr. = 1.5 MeV) search for narrow states (Gamma < 10 MeV) with masses of M_x approx 1500-1850 MeV in ep -> e'K^+ X, e'K^- X and e' pi^+ X electroproduction at small angles and low Q^2 was performed. These states would be candidate partner states of the reported Theta^+(1540) pentaquark. No statistically significant signal was observed in any of the channels at 90% C.L. Upper limits on forward production were determined to be between 0.7% and 4.2% of the Lambda(1520) production cross section, depending on the channel and the assumed mass and width of the state.Comment: 5 pages, 5 figures, to appear in Phys. Rev. C, update with responses to referee suggestion

Quark-Hadron Duality in Neutron (3He) Spin Structure

We present experimental results of the first high-precision test of quark-hadron duality in the spin-structure function g_1 of the neutron and $^3$He using a polarized 3He target in the four-momentum-transfer-squared range from 0.7 to 4.0 (GeV/c)^2. Global duality is observed for the spin-structure function g_1 down to at least Q^2 = 1.8 (GeV/c)^2 in both targets. We have also formed the photon-nucleon asymmetry A_1 in the resonance region for 3He and found no strong Q^2-dependence above 2.2 (GeV/c)^2.Comment: 13 pages, 3 figure

Response theory for time-resolved second-harmonic generation and two-photon photoemission

A unified response theory for the time-resolved nonlinear light generation and two-photon photoemission (2PPE) from metal surfaces is presented. The theory allows to describe the dependence of the nonlinear optical response and the photoelectron yield, respectively, on the time dependence of the exciting light field. Quantum-mechanical interference effects affect the results significantly. Contributions to 2PPE due to the optical nonlinearity of the surface region are derived and shown to be relevant close to a plasmon resonance. The interplay between pulse shape, relaxation times of excited electrons, and band structure is analyzed directly in the time domain. While our theory works for arbitrary pulse shapes, we mainly focus on the case of two pulses of the same mean frequency. Difficulties in extracting relaxation rates from pump-probe experiments are discussed, for example due to the effect of detuning of intermediate states on the interference. The theory also allows to determine the range of validity of the optical Bloch equations and of semiclassical rate equations, respectively. Finally, we discuss how collective plasma excitations affect the nonlinear optical response and 2PPE.Comment: 27 pages, including 11 figures, version as publishe

Moments of the neutron g2g_2 structure function at intermediate Q2Q^2

We present new experimental results of the $^3$He spin structure function $g_2$ in the resonance region at $Q^2$ values between 1.2 and 3.0 (GeV/c)$^2$. Spin dependent moments of the neutron were then extracted. Our main result, the resonance contribution to the neutron $d_2$ matrix element, was found to be small at $$=2.4 (GeV/c)$^2$ and in agreement with the Lattice QCD calculation. The Burkhardt-Cottingham sum rule for $^3$He and the neutron was tested with the measured data and using the Wandzura-Wilczek relation for the low $x$ unmeasured region. A small deviation was observed at $Q^2$ values between 0.5 and 1.2 (GeV/c)$^2$ for the neutron

Parity-Violating Electron Scattering from 4He and the Strange Electric Form Factor of the Nucleon

We have measured the parity-violating electroweak asymmetry in the elastic scattering of polarized electrons from ^4He at an average scattering angle = 5.7 degrees and a four-momentum transfer Q^2 = 0.091 GeV^2. From these data, for the first time, the strange electric form factor of the nucleon G^s_E can be isolated. The measured asymmetry of A_PV = (6.72 +/- 0.84 (stat) +/- 0.21 (syst) parts per million yields a value of G^s_E = -0.038 +/- 0.042 (stat) +/- 0.010 (syst), consistent with zero

Deeply Virtual Compton Scattering off the neutron

The present experiment exploits the interference between the Deeply Virtual Compton Scattering (DVCS) and the Bethe-Heitler processes to extract the imaginary part of DVCS amplitudes on the neutron and on the deuteron from the helicity-dependent D$({\vec e},e'\gamma)X$ cross section measured at $Q^2$=1.9 GeV$^2$ and $x_B$=0.36. We extract a linear combination of generalized parton distributions (GPDs) particularly sensitive to $E_q$, the least constrained GPD. A model dependent constraint on the contribution of the up and down quarks to the nucleon spin is deduced.Comment: Published in Phys. Rev. Let

The E00-110 experiment in Jefferson Lab's Hall A: Deeply Virtual Compton Scattering off the Proton at 6 GeV

We present final results on the photon electroproduction ($\vec{e}p\rightarrow ep\gamma$) cross section in the deeply virtual Compton scattering (DVCS) regime and the valence quark region from Jefferson Lab experiment E00-110. Results from an analysis of a subset of these data were published before, but the analysis has been improved which is described here at length, together with details on the experimental setup. Furthermore, additional data have been analyzed resulting in photon electroproduction cross sections at new kinematic settings, for a total of 588 experimental bins. Results of the $Q^2$- and $x_B$-dependences of both the helicity-dependent and helicity-independent cross sections are discussed. The $Q^2$-dependence illustrates the dominance of the twist-2 handbag amplitude in the kinematics of the experiment, as previously noted. Thanks to the excellent accuracy of this high luminosity experiment, it becomes clear that the unpolarized cross section shows a significant deviation from the Bethe-Heitler process in our kinematics, compatible with a large contribution from the leading twist-2 DVCS$^2$ term to the photon electroproduction cross section. The necessity to include higher-twist corrections in order to fully reproduce the shape of the data is also discussed. The DVCS cross sections in this paper represent the final set of experimental results from E00-110, superseding the previous publication.Comment: 48 pages, 32 figure