H. P. Shanahan

Quenched Light Hadron Spectrum

We present results of a large-scale simulation for the flavor nonsinglet light hadron spectrum in quenched lattice QCD with the Wilson quark action. Hadron masses are calculated at four values of lattice spacing in the range a approximately 0.1-0.05 fm on lattices with a physical extent of 3 fm at five quark masses corresponding to m(pi)/m(rho) approximately 0.75-0.4. The calculated spectrum in the continuum limit shows a systematic deviation from experiment, though the magnitude of deviation is contained within 11%. Results for decay constants and light quark masses are also reported.

Distinct Light-Initiated Gene Expression and Cell Cycle Programs in the Shoot Apex and Cotyledons of Arabidopsis

In darkness, shoot apex growth is repressed, but it becomes rapidly activated by light. We show that phytochromes and cryptochromes play largely redundant roles in this derepression in Arabidopsis thaliana. We examined the light activation of transcriptional changes in a finely resolved time course, comparing the shoot apex (meristem and leaf primordia) and the cotyledon and found >5700 differentially expressed genes. Early events specific to the shoot apices included the repression of genes for Really Interesting New Gene finger proteins and basic domain/leucine zipper and basic helix-loop-helix transcription factors. The downregulation of auxin and ethylene and the upregulation of cytokinin and gibberellin hormonal responses were also characteristic of shoot apices. In the apex, genes involved in ribosome biogenesis and protein translation were rapidly and synchronously induced, simultaneously with cell proliferation genes, preceding visible organ growth. Subsequently, the activation of signaling genes and transcriptional signatures of cell wall expansion, turgor generation, and plastid biogenesis were apparent. Furthermore, light regulates the forms and protein levels of two transcription factors with opposing functions in cell proliferation, E2FB and E2FC, through the Constitutively Photomorphogenic1 (COP1), COP9-Signalosome5, and Deetiolated1 light signaling molecules. These data provide the basis for reconstruction of the regulatory networks for light-regulated meristem, leaf, and cotyledon development.

Jasmonate Controls Leaf Growth by Repressing Cell Proliferation and the Onset of Endoreduplication while Maintaining a Potential Stand-By Mode

The plant hormone jasmonate inhibits leaf growth by delaying the switch from the mitotic cell cycle to the endoreduplication cycle and maintains the cell in a stand-by mode but ready-to-go after the stress. Phytohormones regulate plant growth from cell division to organ development. Jasmonates (JAs) are signaling molecules that have been implicated in stress-induced responses. However, they have also been shown to inhibit plant growth, but the mechanisms are not well understood. The effects of methyl jasmonate (MeJA) on leaf growth regulation were investigated in Arabidopsis (Arabidopsis thaliana) mutants altered in JA synthesis and perception, allene oxide synthase and coi1-16B (for coronatine insensitive1), respectively. We show that MeJA inhibits leaf growth through the JA receptor COI1 by reducing both cell number and size. Further investigations using flow cytometry analyses allowed us to evaluate ploidy levels and to monitor cell cycle progression in leaves and cotyledons of Arabidopsis and/or Nicotiana benthamiana at different stages of development. Additionally, a novel global transcription profiling analysis involving continuous treatment with MeJA was carried out to identify the molecular players whose expression is regulated during leaf development by this hormone and COI1. The results of these studies revealed that MeJA delays the switch from the mitotic cell cycle to the endoreduplication cycle, which accompanies cell expansion, in a COI1-dependent manner and inhibits the mitotic cycle itself, arresting cells in G1 phase prior to the S-phase transition. Significantly, we show that MeJA activates critical regulators of endoreduplication and affects the expression of key determinants of DNA replication. Our discoveries also suggest that MeJA may contribute to the maintenance of a cellular “stand-by mode” by keeping the expression of ribosomal genes at an elevated level. Finally, we propose a novel model for MeJA-regulated COI1-dependent leaf growth inhibition.

Light hadron spectrum and quark masses from quenched lattice QCD

We present the details of simulations for the light hadron spectrum in quenched QCD carried out on the CP-PACS parallel computer. Simulations are made with the Wilson quark action and the plaquette gauge action on lattices of size

Kaon B-parameter from quenched domain-wall QCD

{32}^{3}\ifmmode\times\else\texttimes\fi{}56\char21{}{64}^{3}\ifmmode\times\else\texttimes\fi{}112

Equation of state in finite-temperature QCD with two flavors of improved Wilson quarks

at four values of lattice spacings in the range

Decay constants of B and D mesons from improved relativistic lattice QCD with two flavors of sea quarks

a\ensuremath{\approx}0.1\char21{}0.05\mathrm{fm}

Quenched QCD with O(a) improvement. 1. The Spectrum of light hadrons

and spatial extent

Dynamical quark effects on light quark masses.

{L}_{s}a\ensuremath{\approx}3\mathrm{fm}.

The Isgur-Wise function from the lattice

Hadronic observables are calculated at five quark masses corresponding to