Phage Orf family recombinases:conservation of activities and involvement of the central channel in DNA binding

Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination

Photoproduction of phi(1020) mesons on the proton at large momentum transfer

The cross section for $\phi$ meson photoproduction on the proton has been measured for the first time up to a four-momentum transfer -t = 4 GeV^2, using the CLAS detector at the Thomas Jefferson National Accelerator Facility. At low four-momentum transfer, the differential cross section is well described by Pomeron exchange. At large four-momentum transfer, above -t = 1.8 GeV^2, the data support a model where the Pomeron is resolved into its simplest component, two gluons, which may couple to any quark in the proton and in the $\phi$.Comment: 5 pages; 7 figure

Q^2 Dependence of the S_{11}(1535) Photocoupling and Evidence for a P-wave resonance in eta electroproduction

New cross sections for the reaction $ep \to e'\eta p$ are reported for total center of mass energy $W$=1.5--2.3 GeV and invariant squared momentum transfer $Q^2$=0.13--3.3 GeV$^2$. This large kinematic range allows extraction of new information about response functions, photocouplings, and $\eta N$ coupling strengths of baryon resonances. A sharp structure is seen at $W\sim$ 1.7 GeV. The shape of the differential cross section is indicative of the presence of a $P$-wave resonance that persists to high $Q^2$. Improved values are derived for the photon coupling amplitude for the $S_{11}$(1535) resonance. The new data greatly expands the $Q^2$ range covered and an interpretation of all data with a consistent parameterization is provided.Comment: 31 pages, 9 figure

Deeply virtual and exclusive electroproduction of omega mesons

The exclusive omega electroproduction off the proton was studied in a large kinematical domain above the nucleon resonance region and for the highest possible photon virtuality (Q2) with the 5.75 GeV beam at CEBAF and the CLAS spectrometer. Cross sections were measured up to large values of the four-momentum transfer (-t < 2.7 GeV2) to the proton. The contributions of the interference terms sigma_TT and sigma_TL to the cross sections, as well as an analysis of the omega spin density matrix, indicate that helicity is not conserved in this process. The t-channel pi0 exchange, or more generally the exchange of the associated Regge trajectory, seems to dominate the reaction gamma* p -> omega p, even for Q2 as large as 5 GeV2. Contributions of handbag diagrams, related to Generalized Parton Distributions in the nucleon, are therefore difficult to extract for this process. Remarkably, the high-t behaviour of the cross sections is nearly Q2-independent, which may be interpreted as a coupling of the photon to a point-like object in this kinematical limit.Comment: 15 pages,19 figure

The e p -> e' p eta reaction at and above the S11(1535) baryon resonance

New cross sections for the reaction e p -> ep eta are reported for total center of mass energy W = 1.5--1.86 GeV and invariant momentum transfer Q^2 = 0.25--1.5 GeV^2. This large kinematic range allows extraction of important new information about response functions, photocouplings, and eta N coupling strengths of baryon resonances. Expanded W coverage shows sharp structure at W \~ 1.7 GeV; this is shown to come from interference between S and P waves and can be interpreted in terms of known resonances. Improved values are derived for the photon coupling amplitude for the S11(1535) resonance.Comment: 11 pages, RevTeX, 5 figures, submitted to Phys. Rev. Let

A Precise Measurement of the Neutron Magnetic Form Factor GMn in the Few-GeV2 Region

The neutron elastic magnetic form factor GMn has been extracted from quasielastic electron scattering data on deuterium with the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. The kinematic coverage of the measurement is continuous from Q2=1 GeV2 to 4.8 GeV2. High precision was achieved by employing a ratio technique in which many uncertainties cancel, and by a simultaneous in-situ calibration of the neutron detection efficiency, the largest correction to the data. Neutrons were detected using the CLAS electromagnetic calorimeters and the time-of-flight scintillators. Data were taken at two different electron beam energies, allowing up to four semi-independent measurements of GMn to be made at each value of Q2. The dipole parameterization is found to provide a good description of the data over the measured Q2 range.Comment: 14 pages, 5 figures, revtex4, submitted to Physical Review Letters, Revised version has changes recommended by journal referee

Transverse Polarization of Σ+(1189)\Sigma^{+}(1189) in Photoproduction on a Hydrogen Target in CLAS

Experimental results on the $\Sigma^+(1189)$ hyperon transverse polarization in photoproduction on a hydrogen target using the CLAS detector at Jefferson laboratory are presented. The $\Sigma^+(1189)$ was reconstructed in the exclusive reaction $\gamma+p\rightarrow K^{0}_{S} + \Sigma^+(1189)$ via the $\Sigma^{+} \to p \pi^{0}$ decay mode. The $K^{0}_S$ was reconstructed in the invariant mass of two oppositely charged pions with the $\pi^0$ identified in the missing mass of the detected $p\pi^+\pi^-$ final state. Experimental data were collected in the photon energy range $E_{\gamma}$ = 1.0-3.5 GeV ($\sqrt{s}$ range 1.66-2.73 GeV). We observe a large negative polarization of up to 95%. As the mechanism of transverse polarization of hyperons produced in unpolarized photoproduction experiments is still not well understood, these results will help to distinguish between different theoretical models on hyperon production and provide valuable information for the searches of missing baryon resonances.Comment: pages 1

Measurement of Exclusive π0\pi^0 Electroproduction Structure Functions and their Relationship to Transversity GPDs

Exclusive $\pi^0$ electroproduction at a beam energy of 5.75 GeV has been measured with the Jefferson Lab CLAS spectrometer. Differential cross sections were measured at more than 1800 kinematic values in $Q^2$, $x_B$, $t$, and $\phi_\pi$, in the $Q^2$ range from 1.0 to 4.6 GeV$^2$,\ $-t$ up to 2 GeV$^2$, and $x_B$ from 0.1 to 0.58. Structure functions $\sigma_T +\epsilon \sigma_L, \sigma_{TT}$ and $\sigma_{LT}$ were extracted as functions of $t$ for each of 17 combinations of $Q^2$ and $x_B$. The data were compared directly with two handbag-based calculations including both longitudinal and transversity GPDs. Inclusion of only longitudinal GPDs very strongly underestimates $\sigma_T +\epsilon \sigma_L$ and fails to account for $\sigma_{TT}$ and $\sigma_{LT}$, while inclusion of transversity GPDs brings the calculations into substantially better agreement with the data. There is very strong sensitivity to the relative contributions of nucleon helicity flip and helicity non-flip processes. The results confirm that exclusive $\pi^0$ electroproduction offers direct experimental access to the transversity GPDs.Comment: 6 pages, 2 figure

Q2Q^2 Dependence of Quadrupole Strength in the γ∗p→Δ+(1232)→pπ0\gamma^*p\to\Delta^+(1232)\to p \pi^0 Transition

Models of baryon structure predict a small quadrupole deformation of the nucleon due to residual tensor forces between quarks or distortions from the pion cloud. Sensitivity to quark versus pion degrees of freedom occurs through the $Q^2$ dependence of the magnetic ($M_{1+}$), electric ($E_{1+}$), and scalar ($S_{1+}$) multipoles in the $\gamma^* p \to \Delta^+ \to p \pi^0$ transition. We report new experimental values for the ratios $E_{1+}/M_{1+}$ and $S_{1+}/M_{1+}$ over the range $Q^2$= 0.4-1.8 GeV$^2$, extracted from precision $p(e,e 'p)\pi^{\circ}$ data using a truncated multipole expansion. Results are best described by recent unitary models in which the pion cloud plays a dominant role.Comment: 5 pages, 5 figures, 1 table. To be published in Phys. Rev. Lett. (References, figures and table updated, minor changes.