Identification of differentially expressed genes induced by Bamboo mosaic virus infection in Nicotiana benthamiana by cDNA-amplified fragment length polymorphism

Background: The genes of plants can be up- or down-regulated during viral infection to influence the replication of viruses. Identification of these differentially expressed genes could shed light on the defense systems employed by plants and the mechanisms involved in the adaption of viruses to plant cells. Differential gene expression in Nicotiana benthamiana plants in response to infection with Bamboo mosaic virus (BaMV) was revealed using cDNA-amplified fragment length polymorphism (AFLP). Results: Following inoculation with BaMV, N. benthamiana displayed differential gene expression in response to the infection. Isolation, cloning, and sequencing analysis using cDNA-AFLP furnished 90 cDNA fragments with eight pairs of selective primers. Fifteen randomly selected genes were used for a combined virus-induced gene silencing (VIGS) knockdown experiment, using BaMV infection to investigate the roles played by these genes during viral infection, specifically addressing the means by which these genes influence the accumulation of BaMV protein. Nine of the 15 genes showed either a positive or a negative influence on the accumulation of BaMV protein. Six knockdown plants showed an increase in the accumulation of BaMV, suggesting that they played a role in the resistance to viral infection, while three plants showed a reduction in coat protein, indicating a positive influence on the accumulation of BaMV in plants. An interesting observation was that eight of the nine plants showing an increase in BaMV coat protein were associated with cell rescue, defense, death, aging, signal transduction, and energy production. Conclusions: This study reports an efficient and straightforward method for the identification of host genes involved in viral infection. We succeeded in establishing a cDNA-AFLP system to help track changes in gene expression patterns in N. benthamiana plants when infected with BaMV. The combination of both DNA-AFLP and VIGS methodologies made it possible to screen a large number of genes and identify those associated with infections of plant viruses. In this report, 9 of the 15 analyzed genes exhibited either a positive or a negative influence on the accumulation of BaMV in N. benthamiana plants

B -> J/psi K^* Decays in QCD Factorization

The hadronic decay B -> J K^* is analyzed within the framework of QCD factorization. The spin amplitudes A_0, A_\parallel and A_\perp in the transversity basis and their relative phases are studied using various different form-factor models for B-K^* transition. The effective parameters a_2^h for helicity h=0,+,- states receive different nonfactorizable contributions and hence they are helicity dependent, contrary to naive factorization where a_2^h are universal and polarization independent. QCD factorization breaks down even at the twist-2 level for transverse hard spectator interactions. Although a nontrivial strong phase for the A_\parallel amplitude can be achieved by adjusting the phase of an infrared divergent contribution, the present QCD factorization calculation cannot say anything definite about the phase phi_\parallel. Unlike B -> J/psi K decays, the longitudinal parameter a_2^0 for B -> J/psi K^* does not receive twist-3 corrections and is not large enough to account for the observed branching ratio and the fraction of longitudinal polarization. Possible enhancement mechanisms for a_2^0 are discussed.Comment: 21 pages, 1 figure, a table and a reference added, some typos correcte

Updated Analysis of a_1 and a_2 in Hadronic Two-body Decays of B Mesons

Using the recent experimental data of $B\to D^{(*)}(\pi,\rho)$, $B\to D^{(*)} D_s^{(*)}$, $B\to J/\psi K^{(*)}$ and various model calculations on form factors, we re-analyze the effective coefficients a_1 and a_2 and their ratio. QCD and electroweak penguin corrections to a_1 from $B\to D^{(*)}D_s^{(*)}$ and a_2 from $B\to J/\psi K^{(*)}$ are estimated. In addition to the model-dependent determination, the effective coefficient a_1 is also extracted in a model-independent way as the decay modes $B\to D^{(*)}h$ are related by factorization to the measured semileptonic distribution of $B\to D^{(*)}\ell \bar\nu$ at $q^2=m_h^2$. Moreover, this enables us to extract model-independent heavy-to-heavy form factors, for example, $F_0^{BD}(m_\pi^2)=0.66\pm0.06\pm0.05$ and $A_0^{BD^*}(m_\pi^2)=0.56\pm0.03\pm0.04$. The determination of the magnitude of a_2 from $B\to J/\psi K^{(*)}$ depends on the form factors $F_1^{BK}$, $A_{1,2}^{BK^*}$ and $V^{BK^*}$ at $q^2=m^2_{J/\psi}$. By requiring that a_2 be process insensitive (i.e., the value of a_2 extracted from $J/\psi K$ and $J/\psi K^*$ states should be similar), as implied by the factorization hypothesis, we find that $B\to K^{(*)}$ form factors are severely constrained; they respect the relation $F_1^{BK}(m^2_{J/\psi})\approx 1.9 A_1^{BK^*}(m^2_{J/\psi})$. Form factors $A_2^{BK^*}$ and $V^{BK^*}$ at $q^2=m^2_{J/\psi}$ inferred from the measurements of the longitudinal polarization fraction and the P-wave component in $B\to J/\psi K^*$ are obtained. A stringent upper limit on a_2 is derived from the current bound on \ov B^0\to D^0\pi^0 and it is sensitive to final-state interactions.Comment: 33 pages, 2 figures. Typos in Tables I and IX are corrected. To appear in Phys. Rev.

Vertex functions for d-wave mesons in the light-front approach

While the light-front quark model (LFQM) is employed to calculate hadronic transition matrix elements, the vertex functions must be pre-determined. In this work we derive the vertex functions for all d-wave states in this model. Especially, since both of $^3D_1$ and $^3S_1$ are $1^{--}$ mesons, the Lorentz structures of their vertex functions are the same. Thus when one needs to study the processes where $^3D_1$ is involved, all the corresponding formulas for $^3S_1$ states can be directly applied, only the coefficient of the vertex function should be replaced by that for $^3D_1$. The results would be useful for studying the newly observed resonances which are supposed to be d-wave mesons and furthermore the possible 2S-1D mixing in $\psi'$ with the LFQM.Comment: 12 pages, 2 figures, some typos corrected and more discussions added. Accepted by EPJ

Parity violating target asymmetry in electron - proton scattering

We analyze the parity-violating (PV) components of the analyzing power in elastic electron-proton scattering and discuss their sensitivity to the strange quark contributions to the proton weak form factors. We point out that the component of the analyzing power along the momentum transfer is independent of the electric weak form factor and thus compares favorably with the PV beam asymmetry for a determination of the strangeness magnetic moment. We also show that the transverse component could be used for constraining the strangeness radius. Finally, we argue that a measurement of both components could give experimental information on the strangeness axial charge.Comment: 24 pages, Latex, 5 eps figures, submitted to Phys.Rev.

Nonfactorizable contributions in B decays to charmonium: the case of B−→K−hcB^- \to K^- h_c

Nonleptonic $B$ to charmonium decays generally show deviations from the factorization predictions. For example, the mode $B^- \to K^- \chi_{c0}$ has been experimentally observed with sizeable branching fraction while its factorized amplitude vanishes. We investigate the role of rescattering effects mediated by intermediate charmed meson production in this class of decay modes, and consider $B^- \to K^- h_c$ with $h_c$ the $J^{PC}=1^{+-}$ $\bar c c$ meson. Using an effective lagrangian describing interactions of pairs of heavy-light $Q{\bar q}$ mesons with a quarkonium state, we relate this mode to the analogous mode with $\chi_{c0}$ in the final state. We find ${\cal B}(B^- \to K^- h_c)$ large enough to be measured at the $B$ factories, so that this decay mode could be used to study the poorly known $h_c$.Comment: RevTex, 16 pages, 2 eps figure

BESII Detector Simulation

A Monte Carlo program based on Geant3 has been developed for BESII detector simulation. The organization of the program is outlined, and the digitization procedure for simulating the response of various sub-detectors is described. Comparisons with data show that the performance of the program is generally satisfactory.Comment: 17 pages, 14 figures, uses elsart.cls, to be submitted to NIM

Heavy quarkonium: progress, puzzles, and opportunities

A golden age for heavy quarkonium physics dawned a decade ago, initiated by the confluence of exciting advances in quantum chromodynamics (QCD) and an explosion of related experimental activity. The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress. However, the broad spectrum of subsequent breakthroughs, surprises, and continuing puzzles could only be partially anticipated. Since the release of the YR, the BESII program concluded only to give birth to BESIII; the $B$-factories and CLEO-c flourished; quarkonium production and polarization measurements at HERA and the Tevatron matured; and heavy-ion collisions at RHIC have opened a window on the deconfinement regime. All these experiments leave legacies of quality, precision, and unsolved mysteries for quarkonium physics, and therefore beg for continuing investigations. The plethora of newly-found quarkonium-like states unleashed a flood of theoretical investigations into new forms of matter such as quark-gluon hybrids, mesonic molecules, and tetraquarks. Measurements of the spectroscopy, decays, production, and in-medium behavior of c\bar{c}, b\bar{b}, and b\bar{c} bound states have been shown to validate some theoretical approaches to QCD and highlight lack of quantitative success for others. The intriguing details of quarkonium suppression in heavy-ion collisions that have emerged from RHIC have elevated the importance of separating hot- and cold-nuclear-matter effects in quark-gluon plasma studies. This review systematically addresses all these matters and concludes by prioritizing directions for ongoing and future efforts.Comment: 182 pages, 112 figures. Editors: N. Brambilla, S. Eidelman, B. K. Heltsley, R. Vogt. Section Coordinators: G. T. Bodwin, E. Eichten, A. D. Frawley, A. B. Meyer, R. E. Mitchell, V. Papadimitriou, P. Petreczky, A. A. Petrov, P. Robbe, A. Vair

Pion, kaon, proton and anti-proton transverse momentum distributions from p+p and d+Au collisions at sNN=200\sqrt{s_{NN}} = 200 GeV

Identified mid-rapidity particle spectra of $\pi^{\pm}$, $K^{\pm}$, and $p(\bar{p})$ from 200 GeV p+p and d+Au collisions are reported. A time-of-flight detector based on multi-gap resistive plate chamber technology is used for particle identification. The particle-species dependence of the Cronin effect is observed to be significantly smaller than that at lower energies. The ratio of the nuclear modification factor ($R_{dAu}$) between protons $(p+\bar{p})$ and charged hadrons ($h$) in the transverse momentum range $1.2<{p_{T}}<3.0$ GeV/c is measured to be $1.19\pm0.05$(stat)$\pm0.03$(syst) in minimum-bias collisions and shows little centrality dependence. The yield ratio of $(p+\bar{p})/h$ in minimum-bias d+Au collisions is found to be a factor of 2 lower than that in Au+Au collisions, indicating that the Cronin effect alone is not enough to account for the relative baryon enhancement observed in heavy ion collisions at RHIC.Comment: 6 pages, 4 figures, 1 table. We extended the pion spectra from transverse momentum 1.8 GeV/c to 3. GeV/